Links to Exploration step
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Unequal Recombination and Evolution of the Mating-Type (<italic>MAT</italic>) Loci in the Pathogenic Fungus <italic>Grosmannia clavigera</italic> and Relatives</title><author><name sortKey="Tsui, Clement K M" sort="Tsui, Clement K M" uniqKey="Tsui C" first="Clement K.-M." last="Tsui">Clement K.-M. Tsui</name><affiliation><nlm:aff id="aff1">Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation></author><author><name sortKey="Diguistini, Scott" sort="Diguistini, Scott" uniqKey="Diguistini S" first="Scott" last="Diguistini">Scott Diguistini</name><affiliation><nlm:aff id="aff2">Department of Wood Science, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation></author><author><name sortKey="Wang, Ye" sort="Wang, Ye" uniqKey="Wang Y" first="Ye" last="Wang">Ye Wang</name><affiliation><nlm:aff id="aff2">Department of Wood Science, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation></author><author><name sortKey="Feau, Nicolas" sort="Feau, Nicolas" uniqKey="Feau N" first="Nicolas" last="Feau">Nicolas Feau</name><affiliation><nlm:aff id="aff1">Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation></author><author><name sortKey="Dhillon, Braham" sort="Dhillon, Braham" uniqKey="Dhillon B" first="Braham" last="Dhillon">Braham Dhillon</name><affiliation><nlm:aff id="aff1">Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation></author><author><name sortKey="Bohlmann, Jorg" sort="Bohlmann, Jorg" uniqKey="Bohlmann J" first="Jörg" last="Bohlmann">Jörg Bohlmann</name><affiliation><nlm:aff id="aff1">Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Michael Smith Laboratory, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation></author><author><name sortKey="Hamelin, Richard C" sort="Hamelin, Richard C" uniqKey="Hamelin R" first="Richard C." last="Hamelin">Richard C. Hamelin</name><affiliation><nlm:aff id="aff1">Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation><affiliation><nlm:aff id="aff4">Natural Resources Canada, Laurentian Forestry Centre, Québec, QC, Canada G1V 4C7</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23450093</idno><idno type="pmc">3583454</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583454</idno><idno type="RBID">PMC:3583454</idno><idno type="doi">10.1534/g3.112.004986</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000179</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000179</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Unequal Recombination and Evolution of the Mating-Type (<italic>MAT</italic>) Loci in the Pathogenic Fungus <italic>Grosmannia clavigera</italic> and Relatives</title><author><name sortKey="Tsui, Clement K M" sort="Tsui, Clement K M" uniqKey="Tsui C" first="Clement K.-M." last="Tsui">Clement K.-M. Tsui</name><affiliation><nlm:aff id="aff1">Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation></author><author><name sortKey="Diguistini, Scott" sort="Diguistini, Scott" uniqKey="Diguistini S" first="Scott" last="Diguistini">Scott Diguistini</name><affiliation><nlm:aff id="aff2">Department of Wood Science, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation></author><author><name sortKey="Wang, Ye" sort="Wang, Ye" uniqKey="Wang Y" first="Ye" last="Wang">Ye Wang</name><affiliation><nlm:aff id="aff2">Department of Wood Science, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation></author><author><name sortKey="Feau, Nicolas" sort="Feau, Nicolas" uniqKey="Feau N" first="Nicolas" last="Feau">Nicolas Feau</name><affiliation><nlm:aff id="aff1">Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation></author><author><name sortKey="Dhillon, Braham" sort="Dhillon, Braham" uniqKey="Dhillon B" first="Braham" last="Dhillon">Braham Dhillon</name><affiliation><nlm:aff id="aff1">Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation></author><author><name sortKey="Bohlmann, Jorg" sort="Bohlmann, Jorg" uniqKey="Bohlmann J" first="Jörg" last="Bohlmann">Jörg Bohlmann</name><affiliation><nlm:aff id="aff1">Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Michael Smith Laboratory, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation></author><author><name sortKey="Hamelin, Richard C" sort="Hamelin, Richard C" uniqKey="Hamelin R" first="Richard C." last="Hamelin">Richard C. Hamelin</name><affiliation><nlm:aff id="aff1">Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</nlm:aff></affiliation><affiliation><nlm:aff id="aff4">Natural Resources Canada, Laurentian Forestry Centre, Québec, QC, Canada G1V 4C7</nlm:aff></affiliation></author></analytic><series><title level="j">G3: Genes|Genomes|Genetics</title><idno type="eISSN">2160-1836</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Sexual reproduction in fungi is regulated by the mating-type (<italic>MAT</italic>) locus where recombination is suppressed. We investigated the evolution of <italic>MAT</italic> loci in eight fungal species belonging to <italic>Grosmannia</italic> and <italic>Ophiostoma</italic> (Sordariomycetes, Ascomycota) that include conifer pathogens and beetle symbionts. The <italic>MAT1-2</italic> idiomorph/allele was identified from the assembled and annotated <italic>Grosmannia clavigera</italic> genome, and the <italic>MAT</italic> locus is flanked by genes coding for cytoskeleton protein (<italic>SLA</italic>) and DNA lyase. The synteny of these genes is conserved and consistent with other members in Ascomycota. Using sequences from <italic>SLA</italic> and flanking regions, we characterized the <italic>MAT1-1</italic> idiomorph from other isolates of <italic>G. clavigera</italic> and performed dotplot analysis between the two idiomorphs. Unexpectedly, the <italic>MAT1-2</italic> idiomorph contains a truncated <italic>MAT1-1-1</italic> gene upstream of the <italic>MAT1-2-1</italic> gene that bears the high-mobility-group domain. The nucleotide and amino acid sequence of the truncated <italic>MAT1-1-1</italic> gene is similar to its homologous copy in the <italic>MAT1-1</italic> idiomorph in the opposite mating-type isolate, except that positive selection is acting on the truncated gene and the alpha(α)-box that encodes the transcription factor has been deleted. The <italic>MAT</italic> idiomorphs sharing identical gene organization were present in seven additional species in the Ophiostomatales, suggesting that the presence of truncated <italic>MAT1-1-1</italic> gene is a general pattern in this order. We propose that an ancient unequal recombination event resulted in the ancestral <italic>MAT1-1-1</italic> gene integrated into the <italic>MAT1-2</italic> idiomorph and surviving as the truncated <italic>MAT1-1-1</italic> genes. The α-box domain of <italic>MAT1-1-1</italic> gene, located at the same <italic>MAT</italic> locus adjacent to the <italic>MAT1-2-1</italic> gene, could have been removed by deletion after recombination due to mating signal interference. Our data confirmed a 1:1 MAT/sex ratio in two pathogen populations, and showed that all members of the Ophiostomatales studied here including those that were previously deemed asexual have the potential to reproduce sexually. This ability can potentially increase genetic variability and can enhance fitness in new, ecological niches.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Alamouti, S M" uniqKey="Alamouti S">S. M. Alamouti</name></author><author><name sortKey="Wang, V" uniqKey="Wang V">V. Wang</name></author><author><name sortKey="Diguistini, S" uniqKey="Diguistini S">S. DiGuistini</name></author><author><name sortKey="Six, D" uniqKey="Six D">D. Six</name></author><author><name sortKey="Bohlmann, J" uniqKey="Bohlmann J">J. Bohlmann</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Amselem, J" uniqKey="Amselem J">J. Amselem</name></author><author><name sortKey="Cuomo, C A" uniqKey="Cuomo C">C. A. Cuomo</name></author><author><name sortKey="Van Kan, J A" uniqKey="Van Kan J">J. A. van Kan</name></author><author><name sortKey="Viaud, M" uniqKey="Viaud M">M. Viaud</name></author><author><name sortKey="Benito, E P" uniqKey="Benito E">E. P. Benito</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bennett, R S" uniqKey="Bennett R">R. S. Bennett</name></author><author><name sortKey="Yun, S" uniqKey="Yun S">S. Yun</name></author><author><name sortKey="Lee, T Y" uniqKey="Lee T">T. Y. Lee</name></author><author><name sortKey="Turgeon, B G" uniqKey="Turgeon B">B. G. Turgeon</name></author><author><name sortKey="Arseniuk, E" uniqKey="Arseniuk E">E. Arseniuk</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Billiard, S" uniqKey="Billiard S">S. Billiard</name></author><author><name sortKey="L Pez Villavicencio, M" uniqKey="L Pez Villavicencio M">M. López-Villavicencio</name></author><author><name sortKey="Devier, B" uniqKey="Devier B">B. Devier</name></author><author><name sortKey="Hood, M E" uniqKey="Hood M">M. E. Hood</name></author><author><name sortKey="Fairhead, C" uniqKey="Fairhead C">C. Fairhead</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Billiard, S" uniqKey="Billiard S">S. Billiard</name></author><author><name sortKey="Lopez Villavicencio, M" uniqKey="Lopez Villavicencio M">M. Lopez-Villavicencio</name></author><author><name sortKey="Hood, M E" uniqKey="Hood M">M. E. Hood</name></author><author><name sortKey="Giraud, T" uniqKey="Giraud T">T. Giraud</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brasier, C M" uniqKey="Brasier C">C. M. Brasier</name></author><author><name sortKey="Gibbs, J N" uniqKey="Gibbs J">J. N. Gibbs</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Butler, G" uniqKey="Butler G">G. Butler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carlier, F X" uniqKey="Carlier F">F.-X. Carlier</name></author><author><name sortKey="Decock, C" uniqKey="Decock C">C. Decock</name></author><author><name sortKey="Jacobs, K" uniqKey="Jacobs K">K. Jacobs</name></author><author><name sortKey="Maraite, H" uniqKey="Maraite H">H. Maraite</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Coppin, E" uniqKey="Coppin E">E. Coppin</name></author><author><name sortKey="Debuchy, R" uniqKey="Debuchy R">R. Debuchy</name></author><author><name sortKey="Arnaise, S" uniqKey="Arnaise S">S. Arnaise</name></author><author><name sortKey="Picard, M" uniqKey="Picard M">M. Picard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Coppin, E" uniqKey="Coppin E">E. Coppin</name></author><author><name sortKey="Debuchy, R" uniqKey="Debuchy R">R. Debuchy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Debuchy, R" uniqKey="Debuchy R">R. Debuchy</name></author><author><name sortKey="Turgeon, B G" uniqKey="Turgeon B">B. G. Turgeon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Debuchy, R" uniqKey="Debuchy R">R. Debuchy</name></author><author><name sortKey="Berteaux Lecellier, V" uniqKey="Berteaux Lecellier V">V. Berteaux-Lecellier</name></author><author><name sortKey="Silar, P" uniqKey="Silar P">P. Silar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dereeper, A" uniqKey="Dereeper A">A. Dereeper</name></author><author><name sortKey="Guignon, V" uniqKey="Guignon V">V. Guignon</name></author><author><name sortKey="Blanc, G" uniqKey="Blanc G">G. Blanc</name></author><author><name sortKey="Audic, S" uniqKey="Audic S">S. Audic</name></author><author><name sortKey="Buffet, S" uniqKey="Buffet S">S. Buffet</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Devier, B" uniqKey="Devier B">B. Devier</name></author><author><name sortKey="Aguileta, G" uniqKey="Aguileta G">G. Aguileta</name></author><author><name sortKey="Hood, M E" uniqKey="Hood M">M. E. Hood</name></author><author><name sortKey="Giraud, T" uniqKey="Giraud T">T. Giraud</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Diguistini, S" uniqKey="Diguistini S">S. DiGuistini</name></author><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y. Wang</name></author><author><name sortKey="Liao, N Y" uniqKey="Liao N">N. Y. Liao</name></author><author><name sortKey="Taylor, G" uniqKey="Taylor G">G. Taylor</name></author><author><name sortKey="Tanguay, P" uniqKey="Tanguay P">P. Tanguay</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Farfan, L" uniqKey="Farfan L">L. Farfan</name></author><author><name sortKey="Tsui, C K M" uniqKey="Tsui C">C. K. M. Tsui</name></author><author><name sortKey="El Kassaby, Y A" uniqKey="El Kassaby Y">Y. A. El-Kassaby</name></author><author><name sortKey="Hamelin, R C" uniqKey="Hamelin R">R. C. Hamelin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Felsenstein, J" uniqKey="Felsenstein J">J. Felsenstein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fraser, J A" uniqKey="Fraser J">J. A. Fraser</name></author><author><name sortKey="Stajich, J E" uniqKey="Stajich J">J. E. Stajich</name></author><author><name sortKey="Tarcha, E J" uniqKey="Tarcha E">E. J. Tarcha</name></author><author><name sortKey="Cole, G T" uniqKey="Cole G">G. T. Cole</name></author><author><name sortKey="Inglis, D O" uniqKey="Inglis D">D. O. Inglis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Galagan, J E" uniqKey="Galagan J">J. E. Galagan</name></author><author><name sortKey="Calvo, S E" uniqKey="Calvo S">S. E. Calvo</name></author><author><name sortKey="Cuomo, C" uniqKey="Cuomo C">C. Cuomo</name></author><author><name sortKey="Ma, L J" uniqKey="Ma L">L. J. Ma</name></author><author><name sortKey="Wortman, J R" uniqKey="Wortman J">J. R. Wortman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gioti, A" uniqKey="Gioti A">A. Gioti</name></author><author><name sortKey="Mushegian, A A" uniqKey="Mushegian A">A. A. Mushegian</name></author><author><name sortKey="Strandberg, R" uniqKey="Strandberg R">R. Strandberg</name></author><author><name sortKey="Stajich, J E" uniqKey="Stajich J">J. E. Stajich</name></author><author><name sortKey="Johannesson, H" uniqKey="Johannesson H">H. Johannesson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Glass, N L" uniqKey="Glass N">N. L. Glass</name></author><author><name sortKey="Grotelueschen, J" uniqKey="Grotelueschen J">J. Grotelueschen</name></author><author><name sortKey="Metzenberg, R L" uniqKey="Metzenberg R">R. L. Metzenberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gordon, J L" uniqKey="Gordon J">J. L. Gordon</name></author><author><name sortKey="Armisen, D" uniqKey="Armisen D">D. Armisén</name></author><author><name sortKey="Proux Wera, E" uniqKey="Proux Wera E">E. Proux-Wéra</name></author><author><name sortKey=" Heigeartaigh, S S" uniqKey=" Heigeartaigh S">S. S. Óhéigeartaigh</name></author><author><name sortKey="Byrne, K P" uniqKey="Byrne K">K. P. Byrne</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gorton, C" uniqKey="Gorton C">C. Gorton</name></author><author><name sortKey="Webber, J F" uniqKey="Webber J">J. F. Webber</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="J, Heitman" uniqKey="J H">Heitman J.</name></author><author><name sortKey="Kronstad, J W" uniqKey="Kronstad J">J. W. Kronstad</name></author><author><name sortKey="Taylor, J W" uniqKey="Taylor J">J. W. Taylor</name></author><author><name sortKey="Casselton, L A" uniqKey="Casselton L">L. A. Casselton</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Idnurm, A" uniqKey="Idnurm A">A. Idnurm</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Inderbitzin, P" uniqKey="Inderbitzin P">P. Inderbitzin</name></author><author><name sortKey="Harkness, J" uniqKey="Harkness J">J. Harkness</name></author><author><name sortKey="Turgeon, B G" uniqKey="Turgeon B">B. G. Turgeon</name></author><author><name sortKey="Berbee, M L" uniqKey="Berbee M">M. L. Berbee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jacobi, V" uniqKey="Jacobi V">V. Jacobi</name></author><author><name sortKey="Dufour, J" uniqKey="Dufour J">J. Dufour</name></author><author><name sortKey="Bouvet, G F" uniqKey="Bouvet G">G. F. Bouvet</name></author><author><name sortKey="Aoun, M" uniqKey="Aoun M">M. Aoun</name></author><author><name sortKey="Bernier, L" uniqKey="Bernier L">L. Bernier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jacobs, K" uniqKey="Jacobs K">K. Jacobs</name></author><author><name sortKey="Wingfield, M J" uniqKey="Wingfield M">M. J. Wingfield</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Joly, D L" uniqKey="Joly D">D. L. Joly</name></author><author><name sortKey="Feau, N" uniqKey="Feau N">N. Feau</name></author><author><name sortKey="Tanguay, P" uniqKey="Tanguay P">P. Tanguay</name></author><author><name sortKey="Hamelin, R C" uniqKey="Hamelin R">R. C. Hamelin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kanamori, M" uniqKey="Kanamori M">M. Kanamori</name></author><author><name sortKey="Kato, H" uniqKey="Kato H">H. Kato</name></author><author><name sortKey="Yasuda, N" uniqKey="Yasuda N">N. Yasuda</name></author><author><name sortKey="Koizumi, S" uniqKey="Koizumi S">S. Koizumi</name></author><author><name sortKey="Peever, T L" uniqKey="Peever T">T. L. Peever</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kanematsu, S" uniqKey="Kanematsu S">S. Kanematsu</name></author><author><name sortKey="Adachi, Y" uniqKey="Adachi Y">Y. Adachi</name></author><author><name sortKey="Ito, T" uniqKey="Ito T">T. Ito</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kues, U" uniqKey="Kues U">U. Kües</name></author><author><name sortKey="Yu, Y D" uniqKey="Yu Y">Y.-D. Yu</name></author><author><name sortKey="Navarro Gonzalez, M" uniqKey="Navarro Gonzalez M">M. Navarro-Gonzalez</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kurz, W A" uniqKey="Kurz W">W. A. Kurz</name></author><author><name sortKey="Dymond, C C" uniqKey="Dymond C">C. C. Dymond</name></author><author><name sortKey="Stinson, G" uniqKey="Stinson G">G. Stinson</name></author><author><name sortKey="Rampley, G J" uniqKey="Rampley G">G. J. Rampley</name></author><author><name sortKey="Neilson, E T" uniqKey="Neilson E">E. T. Neilson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lee, S" uniqKey="Lee S">S. Lee</name></author><author><name sortKey="Kim, J" uniqKey="Kim J">J. Kim</name></author><author><name sortKey="Breuil, C" uniqKey="Breuil C">C. Breuil</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lee, S" uniqKey="Lee S">S. Lee</name></author><author><name sortKey="Hamelin, R C" uniqKey="Hamelin R">R. C. Hamelin</name></author><author><name sortKey="Six, D L" uniqKey="Six D">D. L. Six</name></author><author><name sortKey="Breuil, C" uniqKey="Breuil C">C. Breuil</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lim, Y W" uniqKey="Lim Y">Y. W. Lim</name></author><author><name sortKey="Alamouti, S M" uniqKey="Alamouti S">S. M. Alamouti</name></author><author><name sortKey="Kim, J" uniqKey="Kim J">J. Kim</name></author><author><name sortKey="Lee, S" uniqKey="Lee S">S. Lee</name></author><author><name sortKey="Breuil, C" uniqKey="Breuil C">C. Breuil</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lin, X" uniqKey="Lin X">X. Lin</name></author><author><name sortKey="Litvintseva, A P" uniqKey="Litvintseva A">A. P. Litvintseva</name></author><author><name sortKey="Nielsen, K" uniqKey="Nielsen K">K. Nielsen</name></author><author><name sortKey="Patel, S" uniqKey="Patel S">S. Patel</name></author><author><name sortKey="Floyd, A" uniqKey="Floyd A">A. Floyd</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="L Pez Villavicencio, M" uniqKey="L Pez Villavicencio M">M. López-Villavicencio</name></author><author><name sortKey="Aguileta, G" uniqKey="Aguileta G">G. Aguileta</name></author><author><name sortKey="Giraud, T" uniqKey="Giraud T">T. Giraud</name></author><author><name sortKey="De Vienne, D M" uniqKey="De Vienne D">D. M. de Vienne</name></author><author><name sortKey="Lacoste, S" uniqKey="Lacoste S">S. Lacoste</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Menkis, A" uniqKey="Menkis A">A. Menkis</name></author><author><name sortKey="Whittle, C A" uniqKey="Whittle C">C. A. Whittle</name></author><author><name sortKey="Johannesson, H" uniqKey="Johannesson H">H. Johannesson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Metzenberg, R L" uniqKey="Metzenberg R">R. L. Metzenberg</name></author><author><name sortKey="Glass, N L" uniqKey="Glass N">N. L. Glass</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nauta, M J" uniqKey="Nauta M">M. J. Nauta</name></author><author><name sortKey="Hoekstra, H F" uniqKey="Hoekstra H">H. F. Hoekstra</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nygren, K" uniqKey="Nygren K">K. Nygren</name></author><author><name sortKey="Strandberg, R" uniqKey="Strandberg R">R. Strandberg</name></author><author><name sortKey="Wallberg, A" uniqKey="Wallberg A">A. Wallberg</name></author><author><name sortKey="Nabholz, B" uniqKey="Nabholz B">B. Nabholz</name></author><author><name sortKey="Gustafsson, T" uniqKey="Gustafsson T">T. Gustafsson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Paoletti, M" uniqKey="Paoletti M">M. Paoletti</name></author><author><name sortKey="Buck, K W" uniqKey="Buck K">K. W. Buck</name></author><author><name sortKey="Brasier, C M" uniqKey="Brasier C">C. M. Brasier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Paoletti, M" uniqKey="Paoletti M">M. Paoletti</name></author><author><name sortKey="Rydholm, C" uniqKey="Rydholm C">C. Rydholm</name></author><author><name sortKey="Schwier, E U" uniqKey="Schwier E">E. U. Schwier</name></author><author><name sortKey="Anderson, M J" uniqKey="Anderson M">M. J. Anderson</name></author><author><name sortKey="Szakacs, G" uniqKey="Szakacs G">G. Szakacs</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Paoletti, M" uniqKey="Paoletti M">M. Paoletti</name></author><author><name sortKey="Buck, K W" uniqKey="Buck K">K. W. Buck</name></author><author><name sortKey="Brasier, C M" uniqKey="Brasier C">C. M. Brasier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Perkins, D D" uniqKey="Perkins D">D. D. Perkins</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Poggeler, S" uniqKey="Poggeler S">S. Poggeler</name></author><author><name sortKey="O Orman, C M" uniqKey="O Orman C">C. M. O’Gorman</name></author><author><name sortKey="Hoff, B" uniqKey="Hoff B">B. Hoff</name></author><author><name sortKey="Kuck, U" uniqKey="Kuck U">U. Kuck</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Posada, D" uniqKey="Posada D">D. Posada</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Roe, A" uniqKey="Roe A">A. Roe</name></author><author><name sortKey="Rice, S V" uniqKey="Rice S">S. V. Rice</name></author><author><name sortKey="Coltman, D W" uniqKey="Coltman D">D. W. Coltman</name></author><author><name sortKey="Cooke, J E K" uniqKey="Cooke J">J. E. K. Cooke</name></author><author><name sortKey="Sperling, F A H" uniqKey="Sperling F">F. A. H. Sperling</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ropars, J" uniqKey="Ropars J">J. Ropars</name></author><author><name sortKey="Dupont, J" uniqKey="Dupont J">J. Dupont</name></author><author><name sortKey="Fontanillas, E" uniqKey="Fontanillas E">E. Fontanillas</name></author><author><name sortKey="Rodriguez De La Vega, R C" uniqKey="Rodriguez De La Vega R">R. C. Rodríguez de la Vega</name></author><author><name sortKey="Malagnac, F" uniqKey="Malagnac F">F. Malagnac</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rutherford, K" uniqKey="Rutherford K">K. Rutherford</name></author><author><name sortKey="Parkhil, J" uniqKey="Parkhil J">J. Parkhil</name></author><author><name sortKey="Crook, J" uniqKey="Crook J">J. Crook</name></author><author><name sortKey="Horsnell, T" uniqKey="Horsnell T">T. Horsnell</name></author><author><name sortKey="Rice, P" uniqKey="Rice P">P. Rice</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rydholm, C" uniqKey="Rydholm C">C. Rydholm</name></author><author><name sortKey="Dyer, P S" uniqKey="Dyer P">P. S. Dyer</name></author><author><name sortKey="Lutzoni, F" uniqKey="Lutzoni F">F. Lutzoni</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Safranyik, L" uniqKey="Safranyik L">L. Safranyik</name></author><author><name sortKey="Carroll, A L" uniqKey="Carroll A">A. L. Carroll</name></author><author><name sortKey="Regniere, J" uniqKey="Regniere J">J. Régnière</name></author><author><name sortKey="Langor, D W" uniqKey="Langor D">D. W. Langor</name></author><author><name sortKey="Riel, W G" uniqKey="Riel W">W. G. Riel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Seidl, V" uniqKey="Seidl V">V. Seidl</name></author><author><name sortKey="Seibel, C" uniqKey="Seibel C">C. Seibel</name></author><author><name sortKey="Kubicek, C P" uniqKey="Kubicek C">C. P. Kubicek</name></author><author><name sortKey="Schmoll, M" uniqKey="Schmoll M">M. Schmoll</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Solheim, H" uniqKey="Solheim H">H. Solheim</name></author><author><name sortKey="Krokene, P" uniqKey="Krokene P">P. Krokene</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sommerhalder, R J" uniqKey="Sommerhalder R">R. J. Sommerhalder</name></author><author><name sortKey="Mcdonald, B A" uniqKey="Mcdonald B">B. A. Mcdonald</name></author><author><name sortKey="Zhan, J" uniqKey="Zhan J">J. Zhan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Spanu, P D" uniqKey="Spanu P">P. D. Spanu</name></author><author><name sortKey="Abbott, J C" uniqKey="Abbott J">J. C. Abbott</name></author><author><name sortKey="Amselem, J" uniqKey="Amselem J">J. Amselem</name></author><author><name sortKey="Burgis, T A" uniqKey="Burgis T">T. A. Burgis</name></author><author><name sortKey="Soanes, D M" uniqKey="Soanes D">D. M. Soanes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Staden, R" uniqKey="Staden R">R. Staden</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Strandberg, R" uniqKey="Strandberg R">R. Strandberg</name></author><author><name sortKey="Nygren, K" uniqKey="Nygren K">K. Nygren</name></author><author><name sortKey="Menkis, A" uniqKey="Menkis A">A. Menkis</name></author><author><name sortKey="James, T Y" uniqKey="James T">T. Y. James</name></author><author><name sortKey="Wik, L" uniqKey="Wik L">L. Wik</name></author><author><name sortKey="Stajich, J E" uniqKey="Stajich J">J. E. Stajich</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Swofford, D L" uniqKey="Swofford D">D. L. Swofford</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tamura, K" uniqKey="Tamura K">K. Tamura</name></author><author><name sortKey="Peterson, D" uniqKey="Peterson D">D. Peterson</name></author><author><name sortKey="Peterson, N" uniqKey="Peterson N">N. Peterson</name></author><author><name sortKey="Stecher, G" uniqKey="Stecher G">G. Stecher</name></author><author><name sortKey="Nei, M" uniqKey="Nei M">M. Nei</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thompson, J D" uniqKey="Thompson J">J. D. Thompson</name></author><author><name sortKey="Gibson, T J" uniqKey="Gibson T">T. J. Gibson</name></author><author><name sortKey="Plewniak, F" uniqKey="Plewniak F">F. Plewniak</name></author><author><name sortKey="Jeanmougin, F" uniqKey="Jeanmougin F">F. Jeanmougin</name></author><author><name sortKey="Higgins, D G" uniqKey="Higgins D">D. G. Higgins</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tsui, C K M" uniqKey="Tsui C">C. K. M. Tsui</name></author><author><name sortKey="Roe, A D" uniqKey="Roe A">A. D. Roe</name></author><author><name sortKey="El Kassaby, Y A" uniqKey="El Kassaby Y">Y. A. El-Kassaby</name></author><author><name sortKey="Rice, A V" uniqKey="Rice A">A. V. Rice</name></author><author><name sortKey="Alamounti, S M" uniqKey="Alamounti S">S. M. Alamounti</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Turgeon, B G" uniqKey="Turgeon B">B. G. Turgeon</name></author><author><name sortKey="Yoder, O C" uniqKey="Yoder O">O. C. Yoder</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Turgeon, B G" uniqKey="Turgeon B">B. G. Turgeon</name></author><author><name sortKey="Bohlmann, H" uniqKey="Bohlmann H">H. Bohlmann</name></author><author><name sortKey="Ciuffetti, L M" uniqKey="Ciuffetti L">L. M. Ciuffetti</name></author><author><name sortKey="Christiansen, S K" uniqKey="Christiansen S">S. K. Christiansen</name></author><author><name sortKey="Yang, G" uniqKey="Yang G">G. Yang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wilken, P M" uniqKey="Wilken P">P. M. Wilken</name></author><author><name sortKey="Steenkamp, E T" uniqKey="Steenkamp E">E. T. Steenkamp</name></author><author><name sortKey="Hall, T A" uniqKey="Hall T">T. A. Hall</name></author><author><name sortKey="De Beer, Z W" uniqKey="De Beer Z">Z. W. de Beer</name></author><author><name sortKey="Wingfield, M J" uniqKey="Wingfield M">M. J. Wingfield</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Woudenberg, J H C" uniqKey="Woudenberg J">J. H. C. Woudenberg</name></author><author><name sortKey="De Gruyter, J" uniqKey="De Gruyter J">J. de Gruyter</name></author><author><name sortKey="Crous, P W" uniqKey="Crous P">P. W. Crous</name></author><author><name sortKey="Zwiers, L H" uniqKey="Zwiers L">L. H. Zwiers</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yamaoka, Y" uniqKey="Yamaoka Y">Y. Yamaoka</name></author><author><name sortKey="Hiratsuka, Y" uniqKey="Hiratsuka Y">Y. Hiratsuka</name></author><author><name sortKey="Maruyama, P J" uniqKey="Maruyama P">P. J. Maruyama</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, Z" uniqKey="Yang Z">Z. Yang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yokoyama, E" uniqKey="Yokoyama E">E. Yokoyama</name></author><author><name sortKey="Yamagishi, K" uniqKey="Yamagishi K">K. Yamagishi</name></author><author><name sortKey="Hara, A" uniqKey="Hara A">A. Hara</name></author><author><name sortKey="Yokoyama, E" uniqKey="Yokoyama E">E. Yokoyama</name></author><author><name sortKey="Yamagishi, K" uniqKey="Yamagishi K">K. Yamagishi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yokoyama, E" uniqKey="Yokoyama E">E. Yokoyama</name></author><author><name sortKey="Yamagishi, K" uniqKey="Yamagishi K">K. Yamagishi</name></author><author><name sortKey="Hara, A" uniqKey="Hara A">A. Hara</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yun, S H" uniqKey="Yun S">S. H. Yun</name></author><author><name sortKey="Berbee, M L" uniqKey="Berbee M">M. L. Berbee</name></author><author><name sortKey="Yoder, O C" uniqKey="Yoder O">O. C. Yoder</name></author><author><name sortKey="Turgeon, B G" uniqKey="Turgeon B">B. G. Turgeon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zaffarano, P L" uniqKey="Zaffarano P">P. L. Zaffarano</name></author><author><name sortKey="Du, A" uniqKey="Du A">A. Duò</name></author><author><name sortKey="Grunig, C R" uniqKey="Grunig C">C. R. Grünig</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zipfel, R D" uniqKey="Zipfel R">R. D. Zipfel</name></author><author><name sortKey="De Beer, Z W" uniqKey="De Beer Z">Z. W. de Beer</name></author><author><name sortKey="Jacobs, K" uniqKey="Jacobs K">K. Jacobs</name></author><author><name sortKey="Wingfield, B D" uniqKey="Wingfield B">B. D. Wingfield</name></author><author><name sortKey="Wingfield, M J" uniqKey="Wingfield M">M. J. Wingfield</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">G3 (Bethesda)</journal-id><journal-id journal-id-type="iso-abbrev">Genetics</journal-id><journal-id journal-id-type="hwp">G3: Genes, Genomes, Genetics</journal-id><journal-id journal-id-type="pmc">G3: Genes, Genomes, Genetics</journal-id><journal-id journal-id-type="publisher-id">G3: Genes, Genomes, Genetics</journal-id><journal-title-group><journal-title>G3: Genes|Genomes|Genetics</journal-title></journal-title-group><issn pub-type="epub">2160-1836</issn><publisher><publisher-name>Genetics Society of America</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23450093</article-id><article-id pub-id-type="pmc">3583454</article-id><article-id pub-id-type="publisher-id">GGG_004986</article-id><article-id pub-id-type="doi">10.1534/g3.112.004986</article-id><article-categories><subj-group subj-group-type="heading"><subject>Investigations</subject></subj-group></article-categories><title-group><article-title>Unequal Recombination and Evolution of the Mating-Type (<italic>MAT</italic>) Loci in the Pathogenic Fungus <italic>Grosmannia clavigera</italic> and Relatives</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Tsui</surname><given-names>Clement K.-M.</given-names></name><xref ref-type="aff" rid="aff1">*</xref><xref ref-type="corresp" rid="cor1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>DiGuistini</surname><given-names>Scott</given-names></name><xref ref-type="aff" rid="aff2"><sup>†</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Ye</given-names></name><xref ref-type="aff" rid="aff2"><sup>†</sup></xref></contrib><contrib contrib-type="author"><name><surname>Feau</surname><given-names>Nicolas</given-names></name><xref ref-type="aff" rid="aff1">*</xref></contrib><contrib contrib-type="author"><name><surname>Dhillon</surname><given-names>Braham</given-names></name><xref ref-type="aff" rid="aff1">*</xref></contrib><contrib contrib-type="author"><name><surname>Bohlmann</surname><given-names>Jörg</given-names></name><xref ref-type="aff" rid="aff1">*</xref><xref ref-type="aff" rid="aff3"><sup>‡</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hamelin</surname><given-names>Richard C.</given-names></name><xref ref-type="aff" rid="aff1">*</xref><xref ref-type="aff" rid="aff4"><sup>§</sup></xref></contrib><aff id="aff1"><label>*</label>Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</aff><aff id="aff2"><label>†</label>Department of Wood Science, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</aff><aff id="aff3"><label>‡</label>Michael Smith Laboratory, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4</aff><aff id="aff4"><label>§</label>Natural Resources Canada, Laurentian Forestry Centre, Québec, QC, Canada G1V 4C7</aff></contrib-group><author-notes><fn><p>Supporting information is available online at <ext-link ext-link-type="uri" xlink:href="http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.112.004986/-/DC1">http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.112.004986/-/DC1</ext-link></p></fn><fn><p>Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. JX402930−JX402996.</p></fn><corresp id="cor1"><label>1</label>Corresponding author: 2424 Main Mall, Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4. E-mail: <email>clementsui@gmail.com</email></corresp></author-notes><pub-date pub-type="epub"><day>1</day><month>3</month><year>2013</year></pub-date><pub-date pub-type="collection"><month>3</month><year>2013</year></pub-date><volume>3</volume><issue>3</issue><fpage>465</fpage><lpage>480</lpage><history><date date-type="received"><day>14</day><month>11</month><year>2012</year></date><date date-type="accepted"><day>02</day><month>1</month><year>2012</year></date></history><permissions><copyright-statement>Copyright © 2013 Tsui <italic>et al.</italic></copyright-statement><copyright-year>2013</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">http://creativecommons.org/licenses/by/3.0/</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="465.pdf"></self-uri><abstract><p>Sexual reproduction in fungi is regulated by the mating-type (<italic>MAT</italic>) locus where recombination is suppressed. We investigated the evolution of <italic>MAT</italic> loci in eight fungal species belonging to <italic>Grosmannia</italic> and <italic>Ophiostoma</italic> (Sordariomycetes, Ascomycota) that include conifer pathogens and beetle symbionts. The <italic>MAT1-2</italic> idiomorph/allele was identified from the assembled and annotated <italic>Grosmannia clavigera</italic> genome, and the <italic>MAT</italic> locus is flanked by genes coding for cytoskeleton protein (<italic>SLA</italic>) and DNA lyase. The synteny of these genes is conserved and consistent with other members in Ascomycota. Using sequences from <italic>SLA</italic> and flanking regions, we characterized the <italic>MAT1-1</italic> idiomorph from other isolates of <italic>G. clavigera</italic> and performed dotplot analysis between the two idiomorphs. Unexpectedly, the <italic>MAT1-2</italic> idiomorph contains a truncated <italic>MAT1-1-1</italic> gene upstream of the <italic>MAT1-2-1</italic> gene that bears the high-mobility-group domain. The nucleotide and amino acid sequence of the truncated <italic>MAT1-1-1</italic> gene is similar to its homologous copy in the <italic>MAT1-1</italic> idiomorph in the opposite mating-type isolate, except that positive selection is acting on the truncated gene and the alpha(α)-box that encodes the transcription factor has been deleted. The <italic>MAT</italic> idiomorphs sharing identical gene organization were present in seven additional species in the Ophiostomatales, suggesting that the presence of truncated <italic>MAT1-1-1</italic> gene is a general pattern in this order. We propose that an ancient unequal recombination event resulted in the ancestral <italic>MAT1-1-1</italic> gene integrated into the <italic>MAT1-2</italic> idiomorph and surviving as the truncated <italic>MAT1-1-1</italic> genes. The α-box domain of <italic>MAT1-1-1</italic> gene, located at the same <italic>MAT</italic> locus adjacent to the <italic>MAT1-2-1</italic> gene, could have been removed by deletion after recombination due to mating signal interference. Our data confirmed a 1:1 MAT/sex ratio in two pathogen populations, and showed that all members of the Ophiostomatales studied here including those that were previously deemed asexual have the potential to reproduce sexually. This ability can potentially increase genetic variability and can enhance fitness in new, ecological niches.</p></abstract><kwd-group><kwd>heterothallism</kwd><kwd>homothallism</kwd><kwd>mating system evolution</kwd><kwd>outcrossing</kwd><kwd>selfing</kwd></kwd-group><custom-meta-group><custom-meta><meta-name> DJS Export </meta-name><meta-value>v1</meta-value></custom-meta></custom-meta-group></article-meta></front><body><p>Sexual reproduction in fungi is controlled by the mating-type (<italic>MAT</italic>) loci, in which the genes determine mating incompatibility and regulate key mating processes (<xref rid="bib9" ref-type="bibr">Coppin <italic>et al.</italic> 1997</xref>; <xref rid="bib12" ref-type="bibr">Debuchy <italic>et al.</italic> 2010</xref>). Most haploid ascomycete fungi have a single <italic>MAT</italic> locus termed <italic>MAT1</italic>, which has two alleles called <italic>MAT1-1</italic> and <italic>MAT1-2</italic> (<xref rid="bib65" ref-type="bibr">Turgeon and Yoder 2000</xref>). Like large portions of the human X and Y chromosomes, the DNA and amino acid sequences of <italic>MAT1-1</italic> and <italic>MAT1-2</italic> are no more similar than expected by chance; thus, they have been termed idiomorphs (<xref rid="bib40" ref-type="bibr">Metzenberg and Glass 1990</xref>). The idiomorphs encode transcription factors with conserved DNA binding domains involved in the regulation of mating identity and sexual development (<xref rid="bib9" ref-type="bibr">Coppin <italic>et al.</italic> 1997</xref>). The two idiomorphs are distinguished by the presence of either an alpha(α)-box domain in <italic>MAT1-1</italic> or a high-mobility-group (<italic>HMG</italic>) domain in <italic>MAT1-2</italic> (<xref rid="bib9" ref-type="bibr">Coppin <italic>et al.</italic> 1997</xref>). Heterothallic (outcrossing) ascomycete fungi carry either one of the two idiomorphs at the <italic>MAT</italic> locus, and two isolates bearing complementary <italic>MAT1</italic> idiomorphs are required to mate. In contrast, homothallic ascomycetes can undergo haploid selfing (completion of the sexual cycle with a clonemate) because <italic>MAT</italic> genes with α-box and HMG domains are both present in the mating partners (<xref rid="bib12" ref-type="bibr">Debuchy <italic>et al.</italic> 2010</xref>; <xref rid="bib4" ref-type="bibr">Billiard <italic>et al.</italic> 2011</xref>). This gene arrangement may have evolved under selection for universal compatibility (<xref rid="bib4" ref-type="bibr">Billiard <italic>et al.</italic> 2011</xref>, <xref rid="bib5" ref-type="bibr">2012</xref>). The <italic>MAT1-1</italic> idiomorph usually comprises a gene, <italic>MAT1-1-1</italic>, whereas the <italic>MAT1-2</italic> idiomorph has a different gene, <italic>MAT1-2-1</italic>. However, additional genes such as <italic>MAT1-1-2</italic> and <italic>MAT1-1-3</italic> have been reported in the <italic>MAT1-1</italic> idiomorphs in various sordariomycetous ascomycetes (<xref rid="bib65" ref-type="bibr">Turgeon and Yoder 2000</xref>; <xref rid="bib12" ref-type="bibr">Debuchy <italic>et al.</italic> 2010</xref>). The questions of which mode of sexual reproduction, heterothallism or homothallism, is ancestral and which genetic/evolutionary mechanism mediates the change from one to the other have received much attention from fungal biologists (<xref rid="bib12" ref-type="bibr">Debuchy <italic>et al.</italic> 2010</xref>). Therefore, understanding the <italic>MAT</italic> locus organization can provide insight into the genetics and evolution of mating systems and life history in ascomycetes.</p><p>The fungi in Ophiostomatales (Sordariomycetes, Ascomycota) are diverse, with more than 100 species, including many important or aggressive tree pathogens responsible for wilt diseases, blue stain in commercial timber; in addition, they play an important role as insect symbionts and associates, as well as saprophytes (<xref rid="bib75" ref-type="bibr">Zipfel <italic>et al.</italic> 2006</xref>). Most species belong to sexual genera <italic>Grosmannia</italic>, <italic>Ophiostoma</italic>, and the asexual genus <italic>Leptographium</italic>. In North America, <italic>Grosmannia clavigera</italic> is an important conifer pathogen that has a symbiotic relationship with its vector the mountain pine beetle (<italic>Dendroctonus ponderosae</italic>). <italic>Grosmannia clavigera</italic> and other fungal pathogens and symbionts, such as <italic>Leptographium longiclavatum</italic> and <italic>Ophiostoma montium</italic>, are carried in the mycangia and on the exoskeleton of mountain pine beetles because these fungi produce abundant slimy spores that attach themselves to the insect’s body. These fungi can grow into the sapwood and damage the host tree’s water transport system (<xref rid="bib69" ref-type="bibr">Yamaoka <italic>et al.</italic> 1995</xref>; <xref rid="bib56" ref-type="bibr">Solheim and Krokene 1998</xref>). The mountain pine beetles and its fungal symbionts have destroyed more than 17.5 million ha of lodgepole pine forests in western Canada in the last decade (<ext-link ext-link-type="uri" xlink:href="http://www.for.gov.bc.ca/hfp/mountain_pine_beetle/facts.htm">http://www.for.gov.bc.ca/hfp/mountain_pine_beetle/facts.htm</ext-link>), and the magnitude of devastation is the largest in recorded history in Canada (<xref rid="bib33" ref-type="bibr">Kurz <italic>et al.</italic> 2008</xref>; <xref rid="bib54" ref-type="bibr">Safranyik <italic>et al.</italic> 2010</xref>).</p><p><italic>G. clavigera</italic> is very aggressive and it may be capable of detoxifying terpenoids that are an important class of defense compounds in pines (<xref rid="bib15" ref-type="bibr">DiGuistini <italic>et al.</italic> 2011</xref>). Because <italic>G. clavigera</italic> plays an important role in the pine−beetle−fungus dynamics and epidemics, it is essential to understand its biology, genetics, and population structure. Populations of <italic>G. clavigera</italic> are polymorphic and form distinct genetic clusters yet with some gene flow and admixture among clusters (<xref rid="bib35" ref-type="bibr">Lee <italic>et al.</italic> 2007</xref>; <xref rid="bib64" ref-type="bibr">Tsui <italic>et al.</italic> 2012</xref>). Evidence of random mating and linkage equilibrium were also revealed, indicating sexual reproduction occurred in <italic>G. clavigera</italic> populations (<xref rid="bib64" ref-type="bibr">Tsui <italic>et al.</italic> 2012</xref>). However, the sexual fruiting bodies of <italic>G. clavigera</italic> are rarely observed (<xref rid="bib34" ref-type="bibr">Lee <italic>et al.</italic> 2005</xref>), even though <italic>G. clavigera</italic> is reported to have a life cycle comprising both the asexual and sexual stages. It is important to understand the ability of a fungal pathogen to perform sexual reproduction because such information could provide clues to the population biology of these fungi, which could be useful to further our understanding of the recent unprecedented epidemic.</p><p><italic>Grosmannia clavigera</italic> lineage Gs <italic>sensu</italic> (<xref rid="bib1" ref-type="bibr">Alamouti <italic>et al.</italic> 2011</xref>) is heterothallic because a gene homologous to <italic>MAT1-2-1</italic> is characterized at the <italic>MAT</italic> locus in the isolate for which the genome was sequenced but no gene coding for the α-box domain was reported (<xref rid="bib15" ref-type="bibr">DiGuistini <italic>et al.</italic> 2011</xref>). Although fungi in Ophiostomatales are diverse in breeding strategies with worldwide distribution, the <italic>MAT</italic> locus has been characterized in only a limited number of species, such as <italic>Ophiostoma ulmi</italic>, <italic>O. novo-ulmi</italic>, and <italic>O. himal-ulmi</italic>, which are responsible for the Dutch elm disease epidemic in Europe and North America (<xref rid="bib43" ref-type="bibr">Paoletti <italic>et al.</italic> 2005a</xref>; <xref rid="bib27" ref-type="bibr">Jacobi <italic>et al.</italic> 2010</xref>). The genes corresponding to opposite mating-types recently were reported in the <italic>MAT</italic> locus of <italic>Ophiostoma quercus</italic>, which causes significant sapstain in hardwood (<xref rid="bib67" ref-type="bibr">Wilken <italic>et al.</italic> 2012</xref>). Because the <italic>MAT1-1</italic> idiomorph has not been characterized in <italic>G. clavigera</italic> and the <italic>MAT</italic> locus organization has not been well investigated in other fungi of Ophiostomatales, we used genomics and primer walking approaches to study the organization and evolution of the <italic>MAT</italic> locus in <italic>G. clavigera</italic> and eight related fungi. To address the question of whether heterothallism or homothallism is a derived character state, we also compared the <italic>MAT</italic> locus organization with other ascomycete species in the Sordariomycetes. The aim of the present investigation was (1) to characterize the mating-type locus organization of <italic>G. clavigera</italic> bearing a <italic>MAT1-1</italic> idiomorph; (2) to investigate the evolution of <italic>MAT</italic> genes and mating systems in fungi belonging to Ophiostomatales with respect to other ascomycetes; and (3) to determine the mating-type ratio in the populations of <italic>G. clavigera</italic>.</p><sec sec-type="materials|methods" id="s1"><title>Materials and Methods</title><sec id="s2"><title>Fungal materials and culture collection</title><p>Thirty-four fungal isolates belonging to nine species of Ophiostomatales were studied: <italic>G. clavigera</italic> (<italic>Gc</italic>), <italic>L. longiclavatum</italic> (<italic>Llo</italic>), <italic>Leptographium terebrantis</italic> (<italic>Lt</italic>), <italic>Grosmannia aurea</italic> (<italic>Ga</italic>), Leptographium wingfieldii (<italic>Lw</italic>), <italic>Grosmannia robusta</italic> (<italic>Gr</italic>), <italic>Grosmannia huntii</italic> (<italic>Gh</italic>), <italic>Leptographium lundbergii</italic> (<italic>Llun</italic>), and <italic>Ophiostoma montium</italic> (<xref ref-type="table" rid="t1">Table 1</xref>). The identities of many isolates were previously characterized and confirmed using the DNA sequences of rRNA genes and additional protein coding genes (<xref rid="bib36" ref-type="bibr">Lim <italic>et al.</italic> 2004</xref>). They were cultured and maintained in malt extract agar (MEA) (<xref rid="bib64" ref-type="bibr">Tsui <italic>et al.</italic> 2012</xref>). Twenty isolates have <italic>MAT1-1</italic> idiomorphs, and 14 isolates have <italic>MAT1-2</italic> idiomorphs.</p><table-wrap id="t1" position="float"><label>Table 1</label><caption><title>Taxa and isolates used to characterize the mating-type (<italic>MAT</italic>) loci</title></caption><table frame="hsides" rules="groups"><col width="15.02%" span="1"></col><col width="21.66%" span="1"></col><col width="11.73%" span="1"></col><col width="13.98%" span="1"></col><col width="9.68%" span="1"></col><col width="11.71%" span="1"></col><col width="16.22%" span="1"></col><thead><tr><th valign="top" align="left" scope="col" rowspan="1" colspan="1">Species</th><th valign="top" align="center" scope="col" rowspan="1" colspan="1">Isolate Code</th><th valign="top" align="center" scope="col" rowspan="1" colspan="1">Geographic Origin</th><th valign="top" align="center" scope="col" rowspan="1" colspan="1">Substrate</th><th valign="top" align="center" scope="col" rowspan="1" colspan="1">Year of Isolation</th><th valign="top" align="center" scope="col" rowspan="1" colspan="1">Idiomorph</th><th valign="top" align="center" scope="col" rowspan="1" colspan="1">GenBank Accession No.</th></tr></thead><tbody><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><italic>Grosmannia clavigera</italic> (Gc)</td><td valign="top" align="left" rowspan="1" colspan="1">SL-KW1407/UAMH11150
(genome isolate)</td><td valign="top" align="left" rowspan="1" colspan="1">Kamloops, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2001</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">ACXQ02000000 (locus GL629756)</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> B13</td><td valign="top" align="left" rowspan="1" colspan="1">Banff, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2003</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402933</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> SS274</td><td valign="top" align="left" rowspan="1" colspan="1">Fairview, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta × banksiana hybrid</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2007</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402934</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> B101</td><td valign="top" align="left" rowspan="1" colspan="1">Banff, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2003</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402947</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">ATCC18086 (holotype)</td><td valign="top" align="left" rowspan="1" colspan="1">Cache Creek, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus ponderosa</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1965</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402948</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> SS278</td><td valign="top" align="left" rowspan="1" colspan="1">Canmore, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2007</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402945</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> M6</td><td valign="top" align="left" rowspan="1" colspan="1">Manning Park, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2003</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402943</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> M11</td><td valign="top" align="left" rowspan="1" colspan="1">Manning Park, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2003</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402944</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> BW28</td><td valign="top" align="left" rowspan="1" colspan="1">Banff, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2003</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402946</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><italic>Leptographium longiclavatum</italic> (Llo)</td><td valign="top" align="left" rowspan="1" colspan="1"> SS86</td><td valign="top" align="left" rowspan="1" colspan="1">Kakwa, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contora</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2007</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402931</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> HV7</td><td valign="top" align="left" rowspan="1" colspan="1">Hidden Valley, USA</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Dendroctonus ponderosae</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2003</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402932</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> SS88</td><td valign="top" align="left" rowspan="1" colspan="1">Kakwa, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contora</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2007</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402953</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">SL-KW1436 (holotype)</td><td valign="top" align="left" rowspan="1" colspan="1">Williams Lake, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2004</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402954</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> HV18</td><td valign="top" align="left" rowspan="1" colspan="1">Hidden Valley, USA</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Dendroctonus ponderosae</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2003</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402955</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><italic>Leptographium terebrantis</italic> (Lt)</td><td valign="top" align="left" rowspan="1" colspan="1"> T26 (LPKRLT-3)</td><td valign="top" align="left" rowspan="1" colspan="1">BC, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2003</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402936</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> T27 (CBS337.7)</td><td valign="top" align="left" rowspan="1" colspan="1">Louisiana, USA</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus taeda</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1966</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402937</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> SS394</td><td valign="top" align="left" rowspan="1" colspan="1">Fox Creek, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta × banksiana</italic> hybrid</td><td valign="top" align="left" rowspan="1" colspan="1">2007</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402935</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> SS403</td><td valign="top" align="left" rowspan="1" colspan="1">Crowsnest Pass, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2007</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402956</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><italic>Grosmannia aurea</italic> (Ga)</td><td valign="top" align="left" rowspan="1" colspan="1"> SS419</td><td valign="top" align="left" rowspan="1" colspan="1">Grande Prairie, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta × banksiana</italic> hybrid</td><td valign="top" align="left" rowspan="1" colspan="1">2007</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402938</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> SS471</td><td valign="top" align="left" rowspan="1" colspan="1">Fox Creek, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta × banksiana</italic> hybrid</td><td valign="top" align="left" rowspan="1" colspan="1">2007</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402939</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">CBS438.69 (OA18-A27) (holotype)</td><td valign="top" align="left" rowspan="1" colspan="1">Invermore, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta var. latifolia</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1969</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402951</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> AU98-Pr2-169</td><td valign="top" align="left" rowspan="1" colspan="1">Princeton, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta</italic></td><td valign="top" align="left" rowspan="1" colspan="1">NA</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402952</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><italic>Leptographium wingfieldii</italic> (Lw)</td><td valign="top" align="left" rowspan="1" colspan="1"> CMW2095</td><td valign="top" align="left" rowspan="1" colspan="1">NA</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus strobus</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2004</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402950</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> CMW2096</td><td valign="top" align="left" rowspan="1" colspan="1">NA</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus sylvestris</italic></td><td valign="top" align="left" rowspan="1" colspan="1">NA</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402949</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><italic>Leptographium lundbergii</italic> (Llun)</td><td valign="top" align="left" rowspan="1" colspan="1"> UAMH9584</td><td valign="top" align="left" rowspan="1" colspan="1">Skutskar, Uppland, Sweden</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus sylvestris</italic></td><td valign="top" align="left" rowspan="1" colspan="1">NA</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402940</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> UM1434</td><td valign="top" align="left" rowspan="1" colspan="1">NA</td><td valign="top" align="left" rowspan="1" colspan="1">NA</td><td valign="top" align="left" rowspan="1" colspan="1">2004</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402941</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> DAOM64706</td><td valign="top" align="left" rowspan="1" colspan="1">Ontario, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>P. strobus</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1961</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402958</td></tr><tr><td valign="top" align="left" scope="row" rowspan="2" colspan="1"><italic>Grosmannia huntii</italic> (Gh)</td><td valign="top" align="left" rowspan="1" colspan="1"> CBS398.77</td><td valign="top" align="left" rowspan="1" colspan="1">NY</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>P. monticola</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1963</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402942</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"> CMW185</td><td valign="top" align="left" rowspan="1" colspan="1">South Africa</td><td valign="top" align="left" rowspan="1" colspan="1">NA</td><td valign="top" align="left" rowspan="1" colspan="1">2001</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402930</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><italic>Grosmannia robusta</italic> (Gr)</td><td valign="top" align="left" rowspan="1" colspan="1"> CMW668</td><td valign="top" align="left" rowspan="1" colspan="1">South Africa</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Picea abies</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2001</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402957</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><italic>Ophiostoma montium</italic> (Om)</td><td valign="top" align="left" rowspan="1" colspan="1"> UAMH 1363</td><td valign="top" align="left" rowspan="1" colspan="1">British Columbia, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1959</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402993</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> UAMH 4875</td><td valign="top" align="left" rowspan="1" colspan="1">Alberta, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1983</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402995</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> UAMH 11095</td><td valign="top" align="left" rowspan="1" colspan="1">Fox Creek, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta x banksiana</italic> hybrid</td><td valign="top" align="left" rowspan="1" colspan="1">2007</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402994</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"> UAMH 4838</td><td valign="top" align="left" rowspan="1" colspan="1">Alberta, Canada</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>Pinus contorta</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1986</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>MAT1-2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">JX402996</td></tr></tbody></table></table-wrap></sec><sec id="s3"><title>DNA extraction, polymerase chain reaction (PCR) amplification, sequencing</title><p>DNA was extracted from all isolates using the procedures described in <xref rid="bib50" ref-type="bibr">Roe <italic>et al.</italic> (2011)</xref> and <xref rid="bib64" ref-type="bibr">Tsui <italic>et al.</italic> (2012)</xref>. The genome sequencing, assembly, and annotation of <italic>G. clavigera</italic> has been previously described in <xref rid="bib15" ref-type="bibr">DiGuistini <italic>et al.</italic> (2011)</xref>. Based on the genome sequence of <italic>G. clavigera</italic> (GenBank accession number: ACXQ02000000), genes homologous to cytoskeleton assembly protein (<italic>SLA</italic>), HMG-domain of <italic>MAT</italic>, and DNA lyase (<italic>APN</italic>), as well as a few hypothetical proteins without known functions, were identified and characterized (<xref ref-type="fig" rid="fig1">Figure 1</xref>) (<xref rid="bib15" ref-type="bibr">DiGuistini <italic>et al.</italic> 2011</xref>). To characterize the <italic>MAT1-1</italic> idiomorph, we used a long-range PCR amplification approach coupled with primer walking sequencing. Primers ER and UP2-2F targeting the <italic>SLA</italic>, and a hypothetical protein-encoding gene (<italic>CMQ_5208</italic>) located downstream from the <italic>MAT</italic> locus were designed for long-range PCR reaction (<xref ref-type="fig" rid="fig1">Figure 1A</xref>) (<xref ref-type="table" rid="t2">Table 2</xref>). Primers UP2-2R and APN3R, which targeting <italic>CMQ_5208</italic> and <italic>APN</italic>, were also designed to amplify a 15 kb fragment of a putative <italic>MAT1-1</italic> isolate (<xref ref-type="fig" rid="fig1">Figure 1A</xref>).</p><fig id="fig1" fig-type="figure" position="float"><label>Figure 1 </label><caption><p>(A) Sequence arrangement and annotation of the <italic>MAT</italic> idiomorph and adjacent genes from annotated genome of <italic>Grosmannia clavigera</italic> SL-KW1407. (B) The <italic>MAT</italic> genes of opposite mating-type isolates as determined from long-range PCR and primer walking using primers ER and UP2-2F. Genes are indicated by different colors, and the arrows indicate the predicted directions of gene translation. (C) Amplicons of <italic>MAT</italic> fragments after long-range PCR were run in an agarose gel to indicate the size variation between <italic>MAT1-2</italic> and <italic>MAT1-1</italic> isolates.</p></caption><graphic xlink:href="465f1"></graphic></fig><table-wrap id="t2" position="float"><label>Table 2</label><caption><title>Major primers used in this investigation</title></caption><table frame="above" rules="groups"><col width="46.17%" span="1"></col><col width="16.03%" span="1"></col><col width="37.8%" span="1"></col><thead><tr><th valign="top" align="left" scope="col" rowspan="1" colspan="1">Target Gene</th><th valign="top" align="center" scope="col" rowspan="1" colspan="1">Primer Name</th><th valign="top" align="center" scope="col" rowspan="1" colspan="1">Sequence (5′-3′)</th></tr></thead><tbody><tr><td valign="top" align="left" scope="col" rowspan="1" colspan="1">Regular PCR</td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><italic> SLA</italic> of <italic>G. clavigera</italic></td><td valign="top" align="left" rowspan="1" colspan="1">ER</td><td valign="top" align="left" rowspan="1" colspan="1">GCCACGTCGTTCAACAACTA</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> Hypothetical protein (CMQ_5309 of</td><td rowspan="2" valign="top" align="left" colspan="1">UP2-2F</td><td rowspan="2" valign="top" align="left" colspan="1">AGATGGTCATCTCCCGTGAC</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"><italic> G. clavigera</italic>)</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> </td><td valign="top" align="left" rowspan="1" colspan="1">UP2-2R</td><td valign="top" align="left" rowspan="1" colspan="1">AGATGGTCATCTCCCGTGAC</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> HMG domain in <italic>G. clavigera</italic></td><td valign="top" align="left" rowspan="1" colspan="1">HMG1</td><td valign="top" align="left" rowspan="1" colspan="1">CCGCGCCCACCCAATGCGTACAT</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> </td><td valign="top" align="left" rowspan="1" colspan="1">HMG2</td><td valign="top" align="left" rowspan="1" colspan="1">CGAGGGTTGTATCTGTAGTCAGG</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> alpha-box domain in <italic>G. clavigera</italic></td><td valign="top" align="left" rowspan="1" colspan="1">MAT1x1</td><td valign="top" align="left" rowspan="1" colspan="1">CGTCCACTGAATGCCTTCATG</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> </td><td valign="top" align="left" rowspan="1" colspan="1">MAT1x2</td><td valign="top" align="left" rowspan="1" colspan="1">GTGGGCAATCATAGCCAAAGT</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> Cytochrome C oxidase of <italic>G. clavigera</italic></td><td valign="top" align="left" rowspan="1" colspan="1">COX13A</td><td valign="top" align="left" rowspan="1" colspan="1">GCTTGACGCAACTATCTCTGC</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> </td><td valign="top" align="left" rowspan="1" colspan="1">COX13B</td><td valign="top" align="left" rowspan="1" colspan="1">TGCATCCCCTACTCGATACAC</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> DNA lyase (<italic>APN</italic>) of <italic>G. clavigera</italic></td><td valign="top" align="left" rowspan="1" colspan="1">cAPNR</td><td valign="top" align="left" rowspan="1" colspan="1">GATTCCTTTTACAGCTTTCCCCAC</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> </td><td valign="top" align="left" rowspan="1" colspan="1">APN2R</td><td valign="top" align="left" rowspan="1" colspan="1">GACGAGGAGCTGCATCAGG</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> </td><td valign="top" align="left" rowspan="1" colspan="1">APN3F</td><td valign="top" align="left" rowspan="1" colspan="1">GACAGGATCACGAACACAACC</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> </td><td valign="top" align="left" rowspan="1" colspan="1">APN3R</td><td valign="top" align="left" rowspan="1" colspan="1">TCTTCGATTGGCTCTTTAGGG</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><italic> SLA</italic> of <italic>O. montium</italic></td><td valign="top" align="left" rowspan="1" colspan="1">OM7R</td><td valign="top" align="left" rowspan="1" colspan="1">CAACACGCTCATTGAGAC</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> HMG domain in <italic>O. montium</italic></td><td valign="top" align="left" rowspan="1" colspan="1">OM-HMG1</td><td valign="top" align="left" rowspan="1" colspan="1">CGCCCCCCCAATGCCTACATTC</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> </td><td valign="top" align="left" rowspan="1" colspan="1">OM-HMG2</td><td valign="top" align="left" rowspan="1" colspan="1">CGGGGATTGTACTTGTAGTGCGG</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> alpha-box domain in <italic>O. montium</italic></td><td valign="top" align="left" rowspan="1" colspan="1">OM-A1</td><td valign="top" align="left" rowspan="1" colspan="1">GAATGCCTTCATGGCCTTCC</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">OM-A2</td><td valign="top" align="left" rowspan="1" colspan="1">ACCTTTGCCATCAACGTCCATTT</td></tr><tr><td valign="top" align="left" scope="col" rowspan="1" colspan="1">Real-time PCR</td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> truncated <italic>MAT1-1-1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">pMF2</td><td valign="top" align="left" rowspan="1" colspan="1">GATCAGATGGGCAAGCTCAG</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> </td><td valign="top" align="left" rowspan="1" colspan="1">pMR2</td><td valign="top" align="left" rowspan="1" colspan="1">AAGGCTTGGAAGGACGTGTT</td></tr></tbody></table><table-wrap-foot><fn><p>PCR, polymerase chain reaction.</p></fn></table-wrap-foot></table-wrap><p>Long-range PCR amplifications of DNA were carried out in 50 μL using a PTC-100 thermocycler (MJ Research Inc., Watertown, MA). Reaction mixtures contained 100 ng of DNA, 1× PCR buffer, 200 μM each dNTP, 0.6 μM of each primer (Eurofins MWG Operon, Huntsville, AL), 1.5 μL of dimethyl sulfoxide and 2 U of Phusion DNA polymerase (Finnzymes; New England BioLabs, Ipswich, MA). The PCR amplifications were performed for 30 sec at 98°, followed by 35 cycles of 10 sec at 98°, 30 sec at 60−62° and 4 min at 72°, and final extension at 72° for 10 min. Sequencing reactions with primer walking were performed at the Centre de recherche du CHUQ, Québec, Canada. Primers for sequencing are listed in (<ext-link ext-link-type="uri" xlink:href="http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.112.004986/-/DC1/004986SI.pdf">Supporting Information</ext-link>, <ext-link ext-link-type="uri" xlink:href="http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.112.004986/-/DC1/TableS1.xls">Table S1</ext-link>).</p><p>After <italic>MAT</italic> idiomorph characterization, mating-type specific PCR assay was performed by designing primers HMG1 and HMG2 targeting the HMG domain, as well as primers MAT1x1 and MAT1x2 targeting the α-box domain (<xref ref-type="fig" rid="fig1">Figure 1B</xref>, <xref ref-type="table" rid="t2">Table 2</xref>). Fragments of cytochrome c oxidase subunit gene <italic>VIa</italic> (<italic>COX13</italic>) and <italic>APN</italic> also were amplified for selected species and representatives (<xref ref-type="table" rid="t2">Table 2</xref>). PCR amplifications were carried out in 25 μL using a PTC-100 thermocycler (MJ Research Inc.). Reaction mixtures contained 20−40 ng DNA, 1× PCR buffer, 200 μM each dNTP, 1.5 μM of each primer (Eurofins MWG Operon), and 1 U of Paq polymerase (Stratagene, Integrated Sciences). The PCR amplifications were performed for 3 min at 94°, followed by 30 cycles of 35 sec at 94°, 35 sec at 52−55°, and 35 sec at 72°, and final extension at 72° for 7 min.</p></sec><sec id="s4"><title>Gene annotation and analyses</title><p>The genome and transcriptomes of <italic>G. clavigera</italic> were assembled and annotated as described in (<xref rid="bib15" ref-type="bibr">DiGuistini <italic>et al.</italic> 2011</xref>). Gene models were predicted using GLEAN, and the putative gene function assignments were generated from searches of the NCBInr and Swiss-Prot databases using BLAST with PFAM domain assignments (<xref rid="bib15" ref-type="bibr">DiGuistini <italic>et al.</italic> 2011</xref>).</p><p>Sequence reads after primer walking were assembled using the Staden package (<xref rid="bib59" ref-type="bibr">Staden 1996</xref>) and Geneious Pro (<ext-link ext-link-type="uri" xlink:href="http://www.geneious.com/">http://www.geneious.com/</ext-link>), and they were compared with genes present in GenBank using BLASTx and BLASTn. The assembled sequences were submitted to FGENESH+ within Softberry (<ext-link ext-link-type="uri" xlink:href="http://www.softberry.ru/berry.phtml?topic=fgenes_plus&group=programs&subgroup=gfs">http://www.softberry.ru/berry.phtml?topic=fgenes_plus&group=programs&subgroup=gfs</ext-link>) for gene prediction and to determine the location of the coding/non coding regions, and manually annotated with Artemis (<xref rid="bib52" ref-type="bibr">Rutherford <italic>et al.</italic> 2000</xref>).</p><p>The nucleotide sequences of both <italic>MAT</italic> idiomorphs were compared using dotplot (matrix) analyses implemented in Geneious. The sequences of the <italic>MAT</italic> loci were also compared across different species using the online Artemis Comparison Tool (<ext-link ext-link-type="uri" xlink:href="http://www.webact.org/WebACT/home">http://www.webact.org/WebACT/home</ext-link>) with BLASTn algorithm.</p></sec><sec id="s5"><title>Evolutionary analyses of <italic>MAT</italic> genes</title><p>The amino acid sequences encoded by the <italic>MAT1-1</italic> α-box and the <italic>MAT1-2</italic> HMG domain were aligned to sequences of other ascomycetes from GenBank with Clustal W (<xref rid="bib63" ref-type="bibr">Thompson <italic>et al.</italic> 1997</xref>) implemented in Geneious. Phylogenetic analysis was carried out with the Neighbor-joining (NJ) and maximum likelihood algorithm in MEGA 5 (<xref rid="bib62" ref-type="bibr">Tamura <italic>et al.</italic> 2011</xref>), PhyML(<xref rid="bib13" ref-type="bibr">Dereeper <italic>et al.</italic> 2008</xref>) implemented in (<ext-link ext-link-type="uri" xlink:href="http://www.phylogeny.fr/version2_cgi/index.cgi">http://www.phylogeny.fr/version2_cgi/index.cgi</ext-link>), as well as PRODIST and PROML in PHYLIP 3.69 (<xref rid="bib17" ref-type="bibr">Felsenstein 2005</xref>).</p><p>The nucleotide sequences were aligned in Geneious and manually adjusted with Se-Al v2 (<xref rid="bib49" ref-type="bibr">Rambaut 1999</xref>) and analyzed with PAUP v4.b10 (<xref rid="bib61" ref-type="bibr">Swofford 2003</xref>) and MEGA 5 (<xref rid="bib62" ref-type="bibr">Tamura <italic>et al.</italic> 2011</xref>). Nucleotide data of different genes were subjected to parsimony analysis implemented in PAUP. Bootstrap support for the branches was based on 1000 replicates with TBR branch swapping algorithms and simple sequence addition. The individual data sets were also subjected to NJ implemented in PAUP using GTR model corrections with the proportion of variable sites and gamma shape estimated from Modeltest 3.7 (<xref rid="bib48" ref-type="bibr">Posada 2006</xref>). Bootstrap values were estimated based on 1000 replicates. Sequences were deposited in GenBank (accession numbers of <italic>MAT</italic> idiomorphs: JX402930-JX402958, JX402993-JX402996; of other genes: JX402959-JX402992).</p><p>Signatures of purifying or positive selection acting on the <italic>MAT</italic> genes were tested at the codon level. A maximum likelihood analysis was used to fit codon substitution models to the data using the CODEML program within PAML (<xref rid="bib70" ref-type="bibr">Yang 2007</xref>). Four random site models were used to describe the variation of ω (= <italic>dN/dS</italic>) among codon sites in an alignment containing the full length <italic>MAT1-1-1</italic> and truncated <italic>MAT1-1-1</italic> genes of six species. Random site models M1A (neutral), M2A (selection), M7 (beta), and M8 (beta and selection) were used to describe the variation of ω among codon sites within each <italic>MAT1</italic> gene. M1a assumes two site classes in proportions p<sub>0</sub> and p<sub>1</sub> = 1 − p<sub>0</sub> with 0 < ω<sub>0</sub>< 1(purifying selection) and ω<sub>1</sub> = 1 (neutral). M2a adds an additional class of site with ω<sub>2</sub> as a free parameter, allowing for sites with ω<sub>2</sub> > 1 (positive selection) with proportion p<sub>2</sub>. M7 is a flexible null model in which a v ratio for each codon is randomly selected from a beta distribution between 0 and 1. M8 adds one additional site class to M7 allowing for positive selection. A test for positive selection was implemented using likelihood ratio tests that compare models pair M1a/M2a (<xref rid="bib70" ref-type="bibr">Yang 2007</xref>). Three different starting ω values (0.2, 1.0, and 2.0) were implemented for each model fitting, as described in (<xref rid="bib29" ref-type="bibr">Joly <italic>et al.</italic> 2010</xref>). Codon sites under positive selection were then identified using the empirical Bayes method to calculate the posterior probability that a particular amino acid belongs to a given selection class (neutral, deleterious, or advantageous) (<xref rid="bib70" ref-type="bibr">Yang 2007</xref>).</p></sec><sec id="s6"><title>Analysis of mating-type distribution in populations of <italic>G. clavigera</italic> and <italic>L. longiclavatum</italic></title><p>We used the aforementioned mating-type primers (HMG 1, HMG2, MAT1x1, MAT1x2) to identify mating-types in populations from Canada and the USA (<xref ref-type="table" rid="t2">Table 2</xref>). We performed PCR on DNA extracted from 335 isolates of <italic>G. clavigera</italic> characterized in a previous study (<xref rid="bib64" ref-type="bibr">Tsui <italic>et al.</italic> 2012</xref>), as well as more than 100 isolates of <italic>L. longiclavatum</italic> currently being investigated (<xref rid="bib16" ref-type="bibr">Farfan <italic>et al.</italic> 2011</xref>). Mating-type distributions were tested for deviation from the expected ratios of 1:1 using chi-square goodness-of-fit tests.</p></sec><sec id="s7"><title>Reverse transcriptase (RT) quantitative PCR amplification</title><p>RNA was extracted and RT was performed from <italic>G. clavigera</italic> isolate SL-KW1407 cultured on 1% MEA overlaid with cellophane for 4 d (<xref rid="bib15" ref-type="bibr">DiGuistini <italic>et al.</italic> 2011</xref>) to determine the level of expression from hypothetical protein encoding gene <italic>CMQ_5309</italic> (truncated <italic>MAT1-1-1</italic> gene) and <italic>MAT1-2-1</italic>. RT-quantitative PCR was also carried out with SsoFast EvaGreen Supermix (Bio-Rad) in a volume of 20 µL in a Bio-Rad CFX384 system. Primer pairs were internal to regions of <italic>MAT1-2-1</italic> and truncated <italic>MAT1-1-1</italic> to yield amplicons of 100−120 bp (<xref ref-type="table" rid="t2">Table 2</xref>). PCRs were described as follows: 96° for 45 sec, followed by 35 cycles of 95° for 15 sec, and 57.5° for 30 s, followed by a melt-curve analysis. The Cq value for amplification of the β-tubulin gene was used as a reference.</p></sec></sec><sec sec-type="results" id="s8"><title>Results</title><sec id="s9"><title>Organization of the mating-type locus in <italic>G. clavigera</italic></title><p>The <italic>MAT1-2</italic> idiomorph and flanking genes of <italic>G. clavigera</italic> isolate SL-KW1407 were identified from the genome (<xref ref-type="fig" rid="fig1">Figure 1A</xref>), and the amplification of the <italic>MAT1-2</italic> idiomorph from isolate <italic>G. clavigera</italic> SS274 demonstrated greater than 99.9% sequence similarity to the sequence of the reference genome. The gene order and orientation near the <italic>MAT</italic> locus was syntenic with other Sordariomycetes. Two ORFs were predicted in the <italic>MAT1-2</italic> idiomorph. One of the translated proteins bearing the HMG domain (285 amino acids; EFX05114) was homologous to the MAT1-2-1 of other ascomycetes and shared 65% similarity to that of <italic>Ophiostoma himal-ulmi</italic>. In contrast, <italic>CMQ_5309</italic>, encoding a hypothetical protein (EFX04946.1), had no significant similarity to any genes in the NCBI sequence database. <italic>SLA2</italic>, which encodes the cytoskeleton assembly control protein (EFX04935.1), was located upstream from the <italic>MAT</italic> locus, whereas cytochrome c oxidase subunit (EFX05020.1) gene <italic>COX13</italic> and DNA lyase (EFX04950.1) gene <italic>APN2</italic> were located downstream from the MAT (<xref ref-type="fig" rid="fig1">Figure 1A</xref>). The deduced amino acids of <italic>SLA</italic> and <italic>APN</italic> had 68% and 62% identities, respectively, to those of <italic>Neurospora crassa</italic>, a relative in the Sordariomycetes. However, the intergenic distance between <italic>MAT</italic> and <italic>APN</italic> loci in <italic>G. clavigera</italic> was large, spanning greater than 10 kb with several putative proteins coding genes of unknown functions identified (<xref ref-type="fig" rid="fig1">Figure 1A</xref>). One of the putative proteins (CMQ_5213; EFX04951) had a protease-associated domain and was homologous (35% similarity) to a RING-9 protein in <italic>Verticillium albo-atrum</italic> (XP_003007854). The functions of these additional genes to mating activity are not yet established. tBLAST searches using the α-box domain containing genes from different ascomycetes as queries did not return any significant matches in the SL-KW1407 genome, confirming the absence of <italic>MAT1-1-1</italic> gene in the reference isolate.</p><p>Using the primer walking approach, we obtained the full sequence (22,910 bp) of the <italic>MAT1-1</italic> idiomorph of <italic>G. clavigera</italic> isolate B101. The gene arrangement was syntenic to the assembled genome of <italic>G. clavigera</italic> isolate SL-KW1407. The genes of <italic>SLA</italic>, <italic>MAT</italic>, <italic>COX13</italic>, and <italic>APN</italic> were located in the identical order and orientation in both <italic>MAT1-1</italic> and <italic>MAT1-2</italic> idiomorphs. At the nucleotide level, the sequence of the >15-kb fragment spanning from hypothetical protein coding gene <italic>CMQ_5208</italic> to <italic>APN</italic> was 99.9% identical in isolates B101 and SL-KW1407.</p><p>Three open reading frames (ORFs) were predicted in the <italic>MAT1-1</italic> idiomorph of isolate B101, encoding proteins of 619, 340, and 171 amino acids, respectively (<xref ref-type="fig" rid="fig1">Figure 1B</xref>). The first protein had α-box domain and was homologous (52% similarity) to the <italic>MAT1-1-1</italic> (ACZ53927.1) of <italic>Ophiostoma novo-ulmi</italic> subsp. <italic>novo-ulmi</italic>. The second and third proteins were also 24% and 52% similar to the <italic>MAT1-1-2</italic> (ACZ53926.1) and <italic>MAT1-1-3</italic> (ACZ53925.1) of <italic>O</italic>. <italic>novo-ulmi</italic> subsp. <italic>novo-ulmi</italic>, respectively.</p><p>Dotplot comparison of the <italic>MAT1-1</italic> and <italic>MAT1-2</italic> idiomorphs revealed nucleotide sequence similarity (99%) in the SLA encoding gene, regions upstream from the <italic>MAT</italic> locus, as well as the gene encoding protein CMQ_5208 (<xref ref-type="fig" rid="fig2">Figure 2A</xref>). Surprisingly the gene encoding putative protein (CMQ_5309; EFX05047.1) located upstream from the <italic>MAT1-2-1</italic> gene in isolate SL-KW1407 was homologous (>80% similarity in amino acids) to the <italic>MAT1-1-1</italic> gene in the <italic>MAT1-1</italic> idiomorph but shorter in length and without introns. Sequence comparison revealed α-box domain truncation/deletion (89 amino acids) at the N-terminus of the putative protein. The start codon was, however, present in the putative protein coding sequence (now called truncated MAT1-1-1) followed by five codons that are not homologous to the <italic>MAT1-1-1</italic> on the <italic>MAT1-1</italic> idiomorph (<xref ref-type="fig" rid="fig2">Figure 2B</xref>). This 15bp 5′ end sequence was used to search the <italic>G. clavigera</italic> genome as well as the NCBI database but no significant match was returned.</p><fig id="fig2" fig-type="figure" position="float"><label>Figure 2 </label><caption><p>Comparison of <italic>MAT</italic> loci in <italic>Grosmannia clavigera</italic>. (A) Dotplot comparison/pairwise alignment of DNA sequence data for <italic>MAT1-1</italic> and <italic>MAT1-2</italic> idiomorphs of <italic>G. clavigera</italic>. Sequence lengths are given along the axes. (B) The amino acid alignment of MAT1-1-1 in <italic>MAT1-2</italic> idiomorph to the truncated MAT1-1-1 in <italic>MAT1-2</italic> idiomorph of <italic>G. clavigera</italic> by Clustal W. The comparison indicates the deletion of α-box domain (in square) in truncated MAT1-1-1.</p></caption><graphic xlink:href="465f2"></graphic></fig><p>The <italic>MAT</italic> loci of additional <italic>G. clavigera</italic> isolates from different geographic locations were also sequenced using the identical long-range PCR approach to investigate whether the truncated <italic>MAT1-1-1</italic> gene could be unique solely to isolate SL-KW1407 (<xref ref-type="table" rid="t1">Table 1</xref>). Sequencing data confirmed that the isolates bearing the same mating-type have identical idiomorph size (data not shown). The presence of this truncated gene in multiple <italic>G. clavigera</italic> isolates confirms that it is not a spurious result or a unique feature of the reference isolate.</p></sec><sec id="s10"><title>Organization of the <italic>MAT</italic> idiomorphs in fungal species related to <italic>G. clavigera</italic></title><p>The presence of the truncated/incomplete gene suggested that the ancestor of <italic>G. clavigera</italic> may have had both <italic>MAT1-1</italic> and <italic>MAT1-2</italic> copies and was homothallic. To understand the evolutionary history leading to the presence of the truncated <italic>MAT1-1-1</italic> gene, we used the same primer pair ER and UP2-2F (targeting <italic>SLA</italic> and hypothetical protein-coding gene <italic>CMQ_5208</italic>) to characterize the <italic>MAT</italic> loci of several fungi related to <italic>G. clavigera</italic> (<xref rid="bib36" ref-type="bibr">Lim <italic>et al.</italic> 2004</xref>) (<xref ref-type="table" rid="t1">Table 1</xref>). If the truncated gene has been inherited from a common ancestor, it may be preserved in other related species since it may confer an evolutionary or ecological advantage.</p><p>Sequences containing orthologous genes of the <italic>MAT</italic> locus and flanking regions were characterized from 21 isolates belonging to seven species within the Ophiostomatales: <italic>Llo</italic>, <italic>Lw</italic>, <italic>Lt</italic>, <italic>Llun</italic>, <italic>Ga</italic>, <italic>Gr</italic>, and <italic>Gh</italic> (<xref ref-type="table" rid="t1">Table 1</xref>, <xref ref-type="fig" rid="fig1">Figure 1C</xref>). Interspecific variations in fragment size ranged from 5787 to 8011 bp in <italic>MAT1-1</italic> isolates, and from 5209 to 7727 bp in <italic>MAT1-2</italic> isolates among different species. The variations in fragment size are also partly due to incomplete sequencing of the flanking sequences of <italic>SLA</italic> and the putative protein-coding gene <italic>CMQ_5208</italic>. The 3′end of mating-type loci in <italic>Llun</italic> and <italic>Gh</italic> were incomplete because the primers targeting the <italic>CMQ_5208</italic> failed to amplify, and a new primer GCM3 was designed to target the conserved regions in the MAT1-1-3 for <italic>MAT1-1</italic> idiomorph characterization. Conversely, primer HMG2 targeting <italic>MAT1-2-1</italic> gene was used to amplify the partial <italic>MAT1-2</italic> idiomorph fragment. Only the <italic>MAT1-1</italic> idiomorphs of <italic>Lw</italic> and <italic>Gr</italic> were obtained because <italic>MAT1-2</italic> isolates were not available (<xref ref-type="table" rid="t1">Table 1</xref>). The <italic>MAT1-1</italic> idiomorph of <italic>L. lundbergii</italic> isolate DAOM64706 was shorter and incomplete when compared with other taxa, so its sequence was not included in the analyses.</p><p>Dotplot comparison of the <italic>MAT1-1</italic> and <italic>MAT1-2</italic> idiomorphs in each of the species also revealed nucleotide sequence similarity (95–99%) in the SLA protein-coding regions, regions upstream from the <italic>MAT</italic> locus, as well as the <italic>CMQ_5208</italic> (<ext-link ext-link-type="uri" xlink:href="http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.112.004986/-/DC1/FigureS1.pdf">Figure S1</ext-link>). The organization of the idiomorphs among these seven species was identical, with the presence of three predicted ORFs in the <italic>MAT1-1</italic> idiomorph and two ORFs in the <italic>MAT1-2</italic> idiomorph, in addition to the truncated <italic>MAT1-1-1</italic> gene (the comparison among <italic>Gh</italic>, <italic>Gc</italic>, and <italic>Llo</italic> is illustrated in <xref ref-type="fig" rid="fig3">Figure 3</xref>). The nucleotide sequence of the <italic>MAT</italic> idiomorphs was similar among these seven species within <italic>Grosmannia</italic>: it ranged from 72% between <italic>G. clavigera</italic> and <italic>G. huntii</italic> to 97.5% between <italic>G. clavigera</italic> and <italic>L. longiclavatum</italic> (<ext-link ext-link-type="uri" xlink:href="http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.112.004986/-/DC1/TableS2.pdf">Table S2</ext-link> and <xref ref-type="fig" rid="fig3">Figure 3, A and B</xref>). Sequence similarity was much lower when compared to other ascomycetes.</p><fig id="fig3" fig-type="figure" position="float"><label>Figure 3 </label><caption><p>Homology among the <italic>MAT</italic> locus. (A) <italic>MAT1-1</italic> idiomorph; (B) <italic>MAT1-2</italic> idiomorph, of <italic>G. huntii</italic>, <italic>G. clavigera</italic>, and <italic>L. longiclavatum</italic>. The diagram was prepared from the output of Artemis Comparison Tool. Regions of strong homology are shaded and connected by lines. The intensity of shading indicates the strength of homology. Genes are represented by box arrows. The <italic>MAT1-2</italic> sequence of <italic>G. clavigera</italic> SL-KW1407 was obtained from the genome sequence, while the <italic>MAT1-1</italic> sequence of <italic>G. clavigera</italic> and opposite <italic>MAT</italic> isolates of other fungi were obtained in this investigation.</p></caption><graphic xlink:href="465f3"></graphic></fig><p><italic>Ophiostoma</italic> is a sister genus to <italic>Grosmannia</italic> (<xref rid="bib75" ref-type="bibr">Zipfel <italic>et al.</italic> 2006</xref>). A genomic DNA library of <italic>O. montium</italic> populations (R. C. Hamelin, unpublished data) was searched to design primers anchoring the <italic>SLA</italic> and the flanking regions of the <italic>MAT</italic> locus in both mating-types. Using a long-range PCR amplification and primer walking approach, we also amplified the <italic>MAT</italic> locus from four isolates of <italic>O. montium</italic> including both mating-types (<xref ref-type="table" rid="t1">Tables 1</xref> and <xref ref-type="table" rid="t2">2</xref>). We found fragments of ca. 6 kb and 5 kb in size that corresponded to both <italic>MAT1-1</italic> and <italic>MAT1-2</italic> idiomorphs. Dotplot comparison of the <italic>MAT1-1</italic> and <italic>MAT1-2</italic> idiomorphs were similar to the orthologs from <italic>Grosmannia</italic> species and revealed nucleotide sequence similarity in the SLA protein and intergenic regions upstream from the <italic>MAT</italic> locus (<xref ref-type="fig" rid="fig4">Figure 4A</xref>). The <italic>MAT1-1</italic> idiomorph had three putative ORFs that corresponded to <italic>MAT1-1-1</italic>, <italic>MAT1-1-2</italic>, and <italic>MAT1-1-3</italic> genes, and they were similar (53–76% at amino acids level) to those of <italic>O. novo-ulmi</italic> subsp. <italic>novo-ulmi</italic> (<ext-link ext-link-type="uri" xlink:href="http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.112.004986/-/DC1/FigureS2.pdf">Figure S2</ext-link>). The <italic>MAT1-2</italic> idiomorph contained a <italic>MAT1-2-1</italic> gene encoding a protein (263 aa) with HMG domain (75% similar to that of <italic>O. novo-ulmi</italic> subsp. <italic>novo-ulmi)</italic>, as well as a truncated <italic>MAT1-1-1</italic> gene without the α-box domain located upstream from the <italic>MAT1-2-1</italic> gene. The truncated MAT1-1-1 (224 amino acids) was short when compared with the original MAT1-1-1 (714 aa) in the <italic>MAT1-2</italic> idiomorph (<xref ref-type="fig" rid="fig4">Figure 4B</xref>) and the extent of deletion/truncation was greater than that in <italic>Grosmannia</italic> species.</p><fig id="fig4" fig-type="figure" position="float"><label>Figure 4 </label><caption><p>Comparison of <italic>MAT</italic> loci in <italic>Ophiostoma montium</italic>. (A) Dotplot comparison/pairwise alignment of DNA sequence data for <italic>MAT1-1</italic> and <italic>MAT1-2</italic> idiomorphs of <italic>O. montium</italic>. Sequence lengths are given along the axes. (B) The amino acid alignment of MAT1-1-1 in <italic>MAT1-2</italic> idiomorph to the truncated MAT1-1-1 in <italic>MAT1-2</italic> idiomorph of <italic>O. montium</italic> by Clustal W. The comparison indicates the truncated MAT1-1-1 was highly eroded and the absence of α-box domain (in square in full length MAT1-1-1).</p></caption><graphic xlink:href="465f4"></graphic></fig></sec><sec id="s11"><title>Evolutionary analyses of the <italic>MAT</italic> loci</title><p>Phylogenetic analysis inferred from 129 amino acid characters from HMG-domain of 74 ascomycetes supported the monophyletic origin of fungi in Ophiostomatales, and <italic>Grosmannia</italic> and <italic>Ophiostoma</italic> formed a sister relationship with strong statistical support (<xref ref-type="fig" rid="fig5">Figure 5</xref>). Representatives of these two genera also clustered with the members of <italic>Neurospora</italic> and <italic>Sordaria</italic> in Sordariomycetes, with strong likelihood support. Within the cluster of Ophiostomatales, <italic>G. clavigera</italic>, <italic>L. longiclavatum</italic>, and <italic>L. terebrantis</italic> together with either <italic>G. aurea</italic> or <italic>L. wingfieldii</italic> formed a monophyletic clade with >90% bootstrap support. <italic>O. montium</italic> formed a sister relationship to a cluster containing <italic>O. novo-ulmi</italic> and its relatives. <italic>Sporothrix schenckii</italic>, a human pathogen, also nested within the same cluster with strong support (93%). Sequence analysis of α-box domain from 39 ascomycetes species also supported the same sister relationship between <italic>Grosmannia</italic> and <italic>Ophiostoma</italic> but the relationships among the major ascomycete families were not well resolved (<ext-link ext-link-type="uri" xlink:href="http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.112.004986/-/DC1/FigureS3.pdf">Figure S3</ext-link>).</p><fig id="fig5" fig-type="figure" position="float"><label>Figure 5 </label><caption><p>NJ tree generated from MEGA showing the phylogenetic relationships among ascomycetes inferred from the HMG domain (129 amino acid characters) of the MAT1-2-1. Number on branches indicated bootstrap support (1000 pseudoreplicates) more than 60% from NJ and PhyML (from left to right). The taxa shaded in gray indicate the presence of truncated <italic>MAT</italic> genes in opposite <italic>MAT</italic> isolates.</p></caption><graphic xlink:href="465f5"></graphic></fig><p><italic>MAT</italic> genes have been useful for evaluating the phylogenetic relationships among different fungal species (<xref rid="bib11" ref-type="bibr">Debuchy and Turgeon 2006</xref>; <xref rid="bib14" ref-type="bibr">Devier <italic>et al.</italic> 2009</xref>). Gene genealogies of <italic>MAT1-1-2</italic>, <italic>MAT1-1-3</italic>, and <italic>MAT1-2-1</italic> (<ext-link ext-link-type="uri" xlink:href="http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.112.004986/-/DC1/FigureS4.pdf">Figure S4</ext-link>) were concordant with previous species relationships established based on rRNA and other protein coding genes (<xref rid="bib36" ref-type="bibr">Lim <italic>et al.</italic> 2004</xref>). Also, phylogenetic analyses of <italic>SLA</italic>, intergenic regions upstream of full-length <italic>MAT1-1-1</italic> and truncated <italic>MAT1-1-1</italic>, <italic>COX13</italic>, and <italic>APN</italic>, demonstrated that sequences of opposite mating-types corroborate species phylogenies rather than showing <italic>trans</italic>-specific polymorphism (<ext-link ext-link-type="uri" xlink:href="http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.112.004986/-/DC1/FigureS5.pdf">Figure S5</ext-link>). There were no strong conflicts in tree topologies inferred from genes at and flanking the MAT locus. Also there was no conflict in topologies among various tree-building algorithms.</p><p>Phylogenetic analyses of the nucleotide sequences inferred that recombination occurred in the flanking sequences upstream from <italic>MAT1-1-1</italic> and truncated <italic>MAT1-1-1</italic> genes (<xref ref-type="fig" rid="fig6">Figure 6, A and B</xref>). The tree topology of flanking sequence did not conflict with that of SLA coding sequences (<ext-link ext-link-type="uri" xlink:href="http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.112.004986/-/DC1/FigureS5.pdf">Figure S5</ext-link>) because representatives of both mating-types clustered within a species (<xref ref-type="fig" rid="fig6">Figure 6A</xref>). Without recombination, the flanking sequence on <italic>MAT1-1</italic> idiomorph would be expected to cluster separately to the flanking sequence on the <italic>MAT1-2</italic> idiomorph in the gene genealogy. The nucleotide sequence of truncated <italic>MAT1-1-1</italic> genes diverged from the full-length <italic>MAT1-1-1</italic> genes as a result of independent accumulation of mutations (<xref ref-type="fig" rid="fig6">Figure 6B</xref>). Sequences of the opposite mating-type within a species did not cluster together as for the <italic>SLA</italic> gene, but were divergent even though they had high similarity (83%) at the amino acid level.</p><fig id="fig6" fig-type="figure" position="float"><label>Figure 6 </label><caption><p>Gene genealogies showing the phylogenetic relationships between <italic>G. clavigera</italic> and relatives. (A) Intergenic sequences after 3′ end of <italic>SLA</italic> to the 5′ end of the truncated <italic>MAT1-1-1</italic> and <italic>MAT1-1-1</italic> genes (1349 characters), and (B) the full-length and truncated <italic>MAT1-1-1</italic> genes. <italic>MAT1-2</italic> isolates are indicated in green while <italic>MAT1-1</italic> isolates are highlighted in gray (1968 characters). Number on branches indicated bootstrap support (500 pseudoreplicates) greater than 60%.</p></caption><graphic xlink:href="465f6"></graphic></fig><p>Based on the tests of selection using likelihood ratio tests, diversifying (positive) selection was detected in the truncated <italic>MAT1-1-1</italic> from the full-length <italic>MAT1-1-1</italic> at the intraspecific level (<xref ref-type="table" rid="t3">Tables 3</xref>, A and B). The truncated <italic>MAT1-1-1</italic> genes in the <italic>MAT1-2</italic> idiomorph are under positive selection from the full-length <italic>MAT1-1-1</italic> genes on the <italic>MAT1-1</italic> idiomorph in <italic>G. clavigera</italic>, <italic>L. longiclavatum</italic> and <italic>G. aurea</italic>, but not <italic>L. terebrantis</italic> (<xref ref-type="table" rid="t3">Tables 3</xref>, A and B). The truncated/incomplete <italic>MAT1-1-1</italic> gene may go through neutral evolution due to loss of function or adaptive evolution. In contrast, tests of selection on <italic>MAT</italic> genes (<italic>MAT1-2-1</italic>, <italic>MAT1-1-1</italic>, and truncated <italic>MAT1-1-1</italic> individually) at the interspecific level revealed purifying selection (<ext-link ext-link-type="uri" xlink:href="http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.112.004986/-/DC1/TableS3.pdf">Table S3</ext-link>C), indicating that these genes are preserved for proper function of the sexual cycle.</p><table-wrap id="t3" position="float"><label>Table 3</label><caption><title>Parameter estimates and likelihood values of the various models of codon evolution using CODEML in PAML</title></caption><table frame="above" rules="groups"><col width="8.96%" span="1"></col><col width="13.23%" span="1"></col><col width="18.36%" span="1"></col><col width="7.36%" span="1"></col><col width="13.23%" span="1"></col><col width="4.4%" span="1"></col><col width="8.08%" span="1"></col><col width="26.38%" span="1"></col><thead><tr><th valign="top" align="left" scope="col" rowspan="1" colspan="1"></th><th valign="top" align="center" scope="col" rowspan="1" colspan="1">Model</th><th valign="top" align="center" scope="col" rowspan="1" colspan="1">Model Parameters</th><th valign="top" align="center" scope="col" rowspan="1" colspan="1">-lnL</th><th valign="top" align="center" scope="col" rowspan="1" colspan="1">Models Comparison</th><th valign="top" align="center" scope="col" rowspan="1" colspan="1">2ΔL</th><th valign="top" align="center" scope="col" rowspan="1" colspan="1"><italic>Pr.</italic></th><th valign="top" align="center" scope="col" rowspan="1" colspan="1">Sites Under Positive Selection (Bayes Empirical Bayes, Pr. ω>1)</th></tr></thead><tbody><tr><td colspan="8" valign="top" align="left" scope="colgroup" rowspan="1"><bold>A. Test on the truncated and full-length <italic>MAT1-1-1</italic> genes within a species (datasets with positive selection detected)</bold></td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><italic>G. clavigera</italic> (9 isolates)</td><td valign="top" align="center" rowspan="1" colspan="1">M1a (neutral)</td><td valign="top" align="center" rowspan="1" colspan="1"><italic>P<sub>0</sub></italic> = 0.26, <italic>P<sub>1</sub></italic> = 0,74</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2172.75</td><td valign="top" align="center" rowspan="1" colspan="1">M1a <italic>vs.</italic> M2a</td><td valign="top" align="char" char="." rowspan="1" colspan="1">17.70</td><td valign="top" align="center" rowspan="1" colspan="1"><0.001</td><td valign="top" align="center" rowspan="1" colspan="1">2 G (0.99**), 3 I (0.99**), 8 N (0.99**)</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="center" rowspan="1" colspan="1">M2a (selection)</td><td valign="top" align="center" rowspan="1" colspan="1"><italic>P<sub>0</sub></italic> = 0.99, <italic>P<sub>1</sub></italic> = 0.00, <italic>P<sub>2</sub></italic> = 0.004, ω<sub>2</sub> = 227.05</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2163.90</td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="center" rowspan="1" colspan="1">M7 (beta)</td><td valign="top" align="center" rowspan="1" colspan="1"><italic>P</italic> = 2.30, <italic>q</italic> = 0.005</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2172.75</td><td valign="top" align="center" rowspan="1" colspan="1">M7 <italic>vs.</italic> M8</td><td valign="top" align="char" char="." rowspan="1" colspan="1">17.41</td><td valign="top" align="center" rowspan="1" colspan="1"><0.001</td><td valign="top" align="center" rowspan="1" colspan="1">2 G (0.99**), 3 I (0.99**), 8 N (0.99**)</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="center" rowspan="1" colspan="1">M8 (beta + ω)</td><td valign="top" align="center" rowspan="1" colspan="1"><italic>P<sub>0</sub></italic> = 0.98, <italic>P</italic> = 0.005, q = 3.27, <bold><italic>P<sub>1</sub></italic> = 0.02, ω = 81.42</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">2164.05</td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><italic>G. aurea</italic> (four isolates)</td><td valign="top" align="center" rowspan="1" colspan="1">M1a (neutral)</td><td valign="top" align="center" rowspan="1" colspan="1"><italic>P<sub>0</sub></italic> = 0.77, <italic>P<sub>1</sub></italic> = 0.23</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2102.86</td><td valign="top" align="center" rowspan="1" colspan="1">M1a <italic>vs.</italic> M2a</td><td valign="top" align="char" char="." rowspan="1" colspan="1">21.18</td><td valign="top" align="center" rowspan="1" colspan="1"><0.001</td><td valign="top" align="center" rowspan="1" colspan="1">3 A (0.94), 8 A (0.94)</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="center" rowspan="1" colspan="1">M2a (selection)</td><td valign="top" align="center" rowspan="1" colspan="1"><italic>P<sub>0</sub></italic> = 0.99, <italic>P<sub>1</sub></italic> = 0.00, <italic>P<sub>2</sub></italic> = 0.003, ω<sub>2</sub> = 282.78</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2092.27</td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="center" rowspan="1" colspan="1">M7 (beta)</td><td valign="top" align="center" rowspan="1" colspan="1"><italic>P</italic> = 0.005, <italic>q</italic> = 0,012</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2102.96</td><td valign="top" align="center" rowspan="1" colspan="1">M7 <italic>vs.</italic> M8</td><td valign="top" align="char" char="." rowspan="1" colspan="1">21.37</td><td valign="top" align="center" rowspan="1" colspan="1"><0.001</td><td valign="top" align="center" rowspan="1" colspan="1">3 A (0.97*), 8 A (0.97*)</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="center" rowspan="1" colspan="1">M8 (beta + ω)</td><td valign="top" align="center" rowspan="1" colspan="1"><italic>P<sub>0</sub></italic> = 0.99, <italic>P</italic> = 0.005, q = 15.47, <bold><italic>P<sub>1</sub></italic> = 0.003, ω = 282.82</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">2092.27</td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><italic>L. longiclavatum</italic> (five isolates)</td><td valign="top" align="center" rowspan="1" colspan="1">M1a (neutral)</td><td valign="top" align="center" rowspan="1" colspan="1"><italic>P<sub>0</sub></italic> = 0.72, <italic>P<sub>1</sub></italic> = 0.28</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2183.24</td><td valign="top" align="center" rowspan="1" colspan="1">M1a <italic>vs.</italic> M2a</td><td valign="top" align="char" char="." rowspan="1" colspan="1">18.88</td><td valign="top" align="center" rowspan="1" colspan="1"><0.001</td><td valign="top" align="center" rowspan="1" colspan="1">3 A (0.93), 8 A (0,93)</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="center" rowspan="1" colspan="1">M2a (selection)</td><td valign="top" align="center" rowspan="1" colspan="1"><italic>P<sub>0</sub></italic> = 0.99, <italic>P<sub>1</sub></italic> = 0.00, <italic>P<sub>2</sub></italic> = 0.002, ω<sub>2</sub>= 209.51</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2173.80</td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="center" rowspan="1" colspan="1">M7 (beta)</td><td valign="top" align="center" rowspan="1" colspan="1"><italic>P</italic> = 0.005, <italic>q</italic>= 0.011</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2183.25</td><td valign="top" align="center" rowspan="1" colspan="1">M7 <italic>vs.</italic> M8</td><td valign="top" align="char" char="." rowspan="1" colspan="1">18.90</td><td valign="top" align="center" rowspan="1" colspan="1"><0.001</td><td valign="top" align="center" rowspan="1" colspan="1">3 A (0.97*), 8 A (0.97*)</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="center" rowspan="1" colspan="1">M8 (beta + ω)</td><td valign="top" align="center" rowspan="1" colspan="1"><italic>P<sub>0</sub></italic> = 0.99, <italic>P</italic> = 0.51, q = 1.49, <bold><italic>P<sub>1</sub></italic> = 0.001, ω = 209.58</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">2173.80</td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td></tr><tr><td colspan="8" rowspan="1"></td></tr><tr><td colspan="8" valign="top" align="left" scope="col" rowspan="1"><bold>B. Test on the truncated and full-length <italic>MAT1-1-1</italic> genes within a species (dataset without positive selection detected)</bold></td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><italic>L. terebrantis</italic> (4 isolates)</td><td valign="top" align="center" rowspan="1" colspan="1">M1a (neutral)</td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="char" char="." rowspan="1" colspan="1">2462.37</td><td valign="top" align="center" rowspan="1" colspan="1">M1a <italic>vs.</italic> M2a</td><td valign="top" align="center" rowspan="1" colspan="1">1.30</td><td valign="top" align="center" rowspan="1" colspan="1">ns</td><td valign="top" align="left" rowspan="1" colspan="1"></td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="center" rowspan="1" colspan="1">M2a (selection)</td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="char" char="." rowspan="1" colspan="1">2461.72</td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="center" rowspan="1" colspan="1">M7 (beta)</td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="char" char="." rowspan="1" colspan="1">2462.54</td><td valign="top" align="center" rowspan="1" colspan="1">M7 <italic>vs.</italic> M8</td><td valign="top" align="center" rowspan="1" colspan="1">1.65</td><td valign="top" align="center" rowspan="1" colspan="1">ns</td><td valign="top" align="left" rowspan="1" colspan="1"></td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="center" rowspan="1" colspan="1">M8 (beta + ω)</td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="char" char="." rowspan="1" colspan="1">2461.72</td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td></tr></tbody></table><table-wrap-foot><fn><p>Parameter estimates and likelihood values of the various models of codon evolution using CODEML in PAML. Notes <italic>for G. clavigera</italic>: Models assuming positive selection (M2a and M8) fit better the data than neutral models (M1a and M7) according to likelihood ratio tests. Model M2 assumes that 0.4% of the sites have <italic>dN/dS</italic> value = 227.05. Three sites under strong positive selection (<italic>P</italic> > 0.99) are identified by this model with Bayes empirical Bayes methods. Model M8 showed that approximately 98% of sites have <italic>dN/dS</italic> from a U-shaped beta distribution (hence, data fit strongly this model) and approximately 2% of site are under strong positive selection with <italic>dN/dS</italic> = 81.4. Both models M2 and M8 identified the same positive selection sites with Bayes empirical Bayes methods (even if model M8 would assume more sites under positive selection).</p></fn></table-wrap-foot></table-wrap></sec><sec id="s12"><title>Transcript analysis of <italic>MAT</italic> genes</title><p>The <italic>MAT1-1-1</italic> gene with α-box domain is a master regulator of sexual reproduction and is involved in gamete fertilization and the formation of ascogenous hyphae; the deletion of <italic>MAT1-1-1</italic> gene can lead to incomplete development of perithecia in some ascomycetes (<xref rid="bib12" ref-type="bibr">Debuchy <italic>et al.</italic> 2010</xref>). To determine whether the truncated <italic>MAT1-1-1</italic> gene is transcribed, PCR and RT-qPCR experiments were performed on the cDNA. The <italic>MAT1-2-1</italic> gene (Cq = 28) and truncated <italic>MAT1-1-1</italic> gene (Cq = 32.9) were expressed during the vegetative stage in mycelia (4d culture with cellophane overlaid on MEA plates), even though the expression level was low compared with the reference β-tubulin gene (Cq = 25.5). The data were also consistent with the low level of sex gene expression reported in transcriptomic data in various terpenoid compound treatments (<xref rid="bib15" ref-type="bibr">DiGuistini <italic>et al.</italic> 2011</xref>) (<ext-link ext-link-type="uri" xlink:href="http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.112.004986/-/DC1/TableS4.pdf">Table S4</ext-link>).</p></sec><sec id="s13"><title>Determination of MAT type ratio in populations of <italic>G. clavigera</italic> and <italic>L. longiclavatum</italic></title><p>Using specific primers targeting the α-domain and HMG domain, we detected both the <italic>MAT1-1</italic> and <italic>MAT1-2</italic> idiomorphs in <italic>G. clavigera</italic>. We tested the null hypothesis of balanced numbers of the two <italic>MAT</italic> idiomorphs within the epidemic population samples in <xref rid="bib64" ref-type="bibr">Tsui <italic>et al.</italic> (2012)</xref>. Both mating-types were present in the populations at all of the spatial scales. <italic>MAT1-1</italic> and <italic>MAT1-2</italic> frequencies did not significantly deviate from a 1:1 ratio in any of the 19 populations, the four genetic clusters inferred from Bayesian estimation during population genetic studies, nor the entire population (<italic>P</italic> < 0.05) (<xref ref-type="table" rid="t4">Table 4</xref>A). Similarly both <italic>MAT1-1</italic> and <italic>MAT1-2</italic> also were detected in populations of <italic>L. longiclavatum</italic>, and its mating-type ratio did not deviate significantly from 1:1 at small spatial scale (<xref ref-type="table" rid="t4">Table 4</xref>B). However the MAT ratio was significantly different at larger landscape level, where <italic>MAT1-1</italic> isolates appeared more frequent in the Rocky Mountain (Cluster Rocky) whereas <italic>MAT1-2</italic> isolates were predominant in the new epidemics area (Cluster North; northern British Columbia and Alberta) (<xref ref-type="table" rid="t4">Table 4</xref>B).</p><table-wrap id="t4" position="float"><label>Table 4</label><caption><title>MAT ratio tests on populations of <italic>Grosmannia clavigera</italic> and <italic>Leptographium longiclavatum</italic></title></caption><table frame="above" rules="groups"><col width="46.98%" span="1"></col><col width="9.82%" span="1"></col><col width="10.37%" span="1"></col><col width="10.37%" span="1"></col><col width="22.46%" span="1"></col><thead><tr><th valign="top" align="left" scope="col" rowspan="2" colspan="1">Population (Location, Province, or State)</th><th valign="top" align="center" scope="col" rowspan="2" colspan="1">Number Total</th><th colspan="3" valign="top" align="center" scope="colgroup" rowspan="1">Clone Corrected (293 Isolates)<hr></hr></th></tr><tr><th valign="top" align="center" scope="col" rowspan="1" colspan="1"><italic>MAT1-1</italic></th><th valign="top" align="center" scope="col" rowspan="1" colspan="1"><italic>MAT1-2</italic></th><th valign="top" align="center" scope="col" rowspan="1" colspan="1">χ2 (<italic>P</italic> Value)</th></tr></thead><tbody><tr><td colspan="5" valign="top" align="left" scope="colgroup" rowspan="1"><bold>A. MAT ratio of <italic>Grosmannia clavigera</italic> population, including location and sample size (after clone correction) (*<italic>p</italic>< 0.05)</bold></td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Houston, BC</td><td valign="top" align="center" rowspan="1" colspan="1">16</td><td valign="top" align="center" rowspan="1" colspan="1">5</td><td valign="top" align="center" rowspan="1" colspan="1">11</td><td valign="top" align="center" rowspan="1" colspan="1">2.25, <italic>P</italic> = 0.133</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Fort St. James, BC</td><td valign="top" align="center" rowspan="1" colspan="1">23</td><td valign="top" align="center" rowspan="1" colspan="1">13</td><td valign="top" align="center" rowspan="1" colspan="1">10</td><td valign="top" align="center" rowspan="1" colspan="1">0.39, <italic>P</italic> = 0.532</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Tumbler Ridge, BC</td><td valign="top" align="center" rowspan="1" colspan="1">13</td><td valign="top" align="center" rowspan="1" colspan="1">6</td><td valign="top" align="center" rowspan="1" colspan="1">7</td><td valign="top" align="center" rowspan="1" colspan="1">0.0769, <italic>P</italic> = 0.7815</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Fairview, BC</td><td valign="top" align="center" rowspan="1" colspan="1">11</td><td valign="top" align="center" rowspan="1" colspan="1">4</td><td valign="top" align="center" rowspan="1" colspan="1">7</td><td valign="top" align="center" rowspan="1" colspan="1">0.8182, <italic>P</italic> = 0.3657</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Grande Prairie, AB</td><td valign="top" align="center" rowspan="1" colspan="1">20</td><td valign="top" align="center" rowspan="1" colspan="1">8</td><td valign="top" align="center" rowspan="1" colspan="1">12</td><td valign="top" align="center" rowspan="1" colspan="1">0.8, 0.3722</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Fox Creek, AB</td><td valign="top" align="center" rowspan="1" colspan="1">12</td><td valign="top" align="center" rowspan="1" colspan="1">5</td><td valign="top" align="center" rowspan="1" colspan="1">7</td><td valign="top" align="center" rowspan="1" colspan="1">0.333, 0.5637</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Kakwa, AB</td><td valign="top" align="center" rowspan="1" colspan="1">17</td><td valign="top" align="center" rowspan="1" colspan="1">5</td><td valign="top" align="center" rowspan="1" colspan="1">12</td><td valign="top" align="center" rowspan="1" colspan="1">2.8824, 0.08956</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Valemount, BC</td><td valign="top" align="center" rowspan="1" colspan="1">8</td><td valign="top" align="center" rowspan="1" colspan="1">4</td><td valign="top" align="center" rowspan="1" colspan="1">4</td><td valign="top" align="center" rowspan="1" colspan="1">0,1</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Williams Lake, BC</td><td valign="top" align="center" rowspan="1" colspan="1">15</td><td valign="top" align="center" rowspan="1" colspan="1">4</td><td valign="top" align="center" rowspan="1" colspan="1">11</td><td valign="top" align="center" rowspan="1" colspan="1">3.2667, 0.0707</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Manning Park, BC</td><td valign="top" align="center" rowspan="1" colspan="1">19</td><td valign="top" align="center" rowspan="1" colspan="1">10</td><td valign="top" align="center" rowspan="1" colspan="1">9</td><td valign="top" align="center" rowspan="1" colspan="1">0.0526, 0.8185</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Golden, BC</td><td valign="top" align="center" rowspan="1" colspan="1">8</td><td valign="top" align="center" rowspan="1" colspan="1">4</td><td valign="top" align="center" rowspan="1" colspan="1">4</td><td valign="top" align="center" rowspan="1" colspan="1">0,1</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Yoho, BC</td><td valign="top" align="center" rowspan="1" colspan="1">7</td><td valign="top" align="center" rowspan="1" colspan="1">3</td><td valign="top" align="center" rowspan="1" colspan="1">4</td><td valign="top" align="center" rowspan="1" colspan="1">0.1429, 0.7055</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Banff, AB</td><td valign="top" align="center" rowspan="1" colspan="1">20</td><td valign="top" align="center" rowspan="1" colspan="1">11</td><td valign="top" align="center" rowspan="1" colspan="1">9</td><td valign="top" align="center" rowspan="1" colspan="1">0.2, 0.6547</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Canmore, AB</td><td valign="top" align="center" rowspan="1" colspan="1">39</td><td valign="top" align="center" rowspan="1" colspan="1">14</td><td valign="top" align="center" rowspan="1" colspan="1">25</td><td valign="top" align="center" rowspan="1" colspan="1">3.1026, 0.07817</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Cypress Hills, AB</td><td valign="top" align="center" rowspan="1" colspan="1">5</td><td valign="top" align="center" rowspan="1" colspan="1">2</td><td valign="top" align="center" rowspan="1" colspan="1">3</td><td valign="top" align="center" rowspan="1" colspan="1">0.2, 0.6547</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Sparwood, BC</td><td valign="top" align="center" rowspan="1" colspan="1">7</td><td valign="top" align="center" rowspan="1" colspan="1">3</td><td valign="top" align="center" rowspan="1" colspan="1">4</td><td valign="top" align="center" rowspan="1" colspan="1">0.1429,0.7055</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Crowsnest Pass, AB</td><td valign="top" align="center" rowspan="1" colspan="1">9</td><td valign="top" align="center" rowspan="1" colspan="1">5</td><td valign="top" align="center" rowspan="1" colspan="1">4</td><td valign="top" align="center" rowspan="1" colspan="1">0.1111,0.7389</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Hidden Valley, MT, USA</td><td valign="top" align="center" rowspan="1" colspan="1">20</td><td valign="top" align="center" rowspan="1" colspan="1">11</td><td valign="top" align="center" rowspan="1" colspan="1">9</td><td valign="top" align="center" rowspan="1" colspan="1">0.2, 0.6547</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Hell Roaring, ID, USA</td><td valign="top" align="center" rowspan="1" colspan="1">24</td><td valign="top" align="center" rowspan="1" colspan="1">15</td><td valign="top" align="center" rowspan="1" colspan="1">9</td><td valign="top" align="center" rowspan="1" colspan="1">1.5, 0.2207</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><bold>Total</bold></td><td valign="top" align="center" rowspan="1" colspan="1">293</td><td valign="top" align="center" rowspan="1" colspan="1">132</td><td valign="top" align="center" rowspan="1" colspan="1">161</td><td valign="top" align="center" rowspan="1" colspan="1">2.8703, 0.09023</td></tr><tr><td valign="top" align="left" scope="col" rowspan="1" colspan="1">Genetic clusters inferred from <xref rid="bib64" ref-type="bibr">Tsui <italic>et al.</italic> (2012)</xref></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> NBC</td><td valign="top" align="center" rowspan="1" colspan="1">39</td><td valign="top" align="center" rowspan="1" colspan="1">18</td><td valign="top" align="center" rowspan="1" colspan="1">21</td><td valign="top" align="center" rowspan="1" colspan="1">0.231,0.63</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> NORTH</td><td valign="top" align="center" rowspan="1" colspan="1">81</td><td valign="top" align="center" rowspan="1" colspan="1">32</td><td valign="top" align="center" rowspan="1" colspan="1">49</td><td valign="top" align="center" rowspan="1" colspan="1">3.57, 0.059</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> SBC</td><td valign="top" align="center" rowspan="1" colspan="1">34</td><td valign="top" align="center" rowspan="1" colspan="1">14</td><td valign="top" align="center" rowspan="1" colspan="1">20</td><td valign="top" align="center" rowspan="1" colspan="1">1.059, 0.303</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> ROCKY</td><td valign="top" align="center" rowspan="1" colspan="1">139</td><td valign="top" align="center" rowspan="1" colspan="1">68</td><td valign="top" align="center" rowspan="1" colspan="1">71</td><td valign="top" align="center" rowspan="1" colspan="1">0.065, 0799</td></tr><tr><td colspan="5" rowspan="1"></td></tr><tr><td colspan="5" valign="top" align="center" scope="col" rowspan="1"><bold>B. MAT ratio of <italic>Leptogaphium longiclavatum</italic> populations, including locations and sample size (after clone correction) (*<italic>p</italic><0.05)</bold></td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Canmore</td><td valign="top" align="center" rowspan="1" colspan="1">15</td><td valign="top" align="center" rowspan="1" colspan="1">4</td><td valign="top" align="center" rowspan="1" colspan="1">11</td><td valign="top" align="center" rowspan="1" colspan="1">3.27, 0.07</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Crownsnest Pass</td><td valign="top" align="center" rowspan="1" colspan="1">6</td><td valign="top" align="center" rowspan="1" colspan="1">2</td><td valign="top" align="center" rowspan="1" colspan="1">4</td><td valign="top" align="center" rowspan="1" colspan="1">0.667, 0.414</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Cypress Hills</td><td valign="top" align="center" rowspan="1" colspan="1">2</td><td valign="top" align="center" rowspan="1" colspan="1">1</td><td valign="top" align="center" rowspan="1" colspan="1">1</td><td valign="top" align="center" rowspan="1" colspan="1">0, 1</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Golden</td><td valign="top" align="center" rowspan="1" colspan="1">8</td><td valign="top" align="center" rowspan="1" colspan="1">3</td><td valign="top" align="center" rowspan="1" colspan="1">5</td><td valign="top" align="center" rowspan="1" colspan="1">0.5, 0.48</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Sparwood</td><td valign="top" align="center" rowspan="1" colspan="1">7</td><td valign="top" align="center" rowspan="1" colspan="1">3</td><td valign="top" align="center" rowspan="1" colspan="1">4</td><td valign="top" align="center" rowspan="1" colspan="1">0.143, 0.705</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Yoho</td><td valign="top" align="center" rowspan="1" colspan="1">5</td><td valign="top" align="center" rowspan="1" colspan="1">2</td><td valign="top" align="center" rowspan="1" colspan="1">3</td><td valign="top" align="center" rowspan="1" colspan="1">0.2, 0.655</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1">Cluster Rocky</td><td valign="top" align="center" rowspan="1" colspan="1">43</td><td valign="top" align="center" rowspan="1" colspan="1">15</td><td valign="top" align="center" rowspan="1" colspan="1">28</td><td valign="top" align="center" rowspan="1" colspan="1">3.93, 0.047*</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> Fairview</td><td valign="top" align="center" rowspan="1" colspan="1">15</td><td valign="top" align="center" rowspan="1" colspan="1">9</td><td valign="top" align="center" rowspan="1" colspan="1">6</td><td valign="top" align="center" rowspan="1" colspan="1">0.6, 0.439</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> Fox Creek</td><td valign="top" align="center" rowspan="1" colspan="1">21</td><td valign="top" align="center" rowspan="1" colspan="1">12</td><td valign="top" align="center" rowspan="1" colspan="1">9</td><td valign="top" align="center" rowspan="1" colspan="1">0.429, 0.512</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> Grande Prairies</td><td valign="top" align="center" rowspan="1" colspan="1">29</td><td valign="top" align="center" rowspan="1" colspan="1">19</td><td valign="top" align="center" rowspan="1" colspan="1">10</td><td valign="top" align="center" rowspan="1" colspan="1">2.793, 0.09</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> Kakwa</td><td valign="top" align="center" rowspan="1" colspan="1">22</td><td valign="top" align="center" rowspan="1" colspan="1">11</td><td valign="top" align="center" rowspan="1" colspan="1">11</td><td valign="top" align="center" rowspan="1" colspan="1">0, 1</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> Tumbler Ridge</td><td valign="top" align="center" rowspan="1" colspan="1">26</td><td valign="top" align="center" rowspan="1" colspan="1">16</td><td valign="top" align="center" rowspan="1" colspan="1">10</td><td valign="top" align="center" rowspan="1" colspan="1">1.385, 0.239</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> Valemount</td><td valign="top" align="center" rowspan="1" colspan="1">7</td><td valign="top" align="center" rowspan="1" colspan="1">4</td><td valign="top" align="center" rowspan="1" colspan="1">3</td><td valign="top" align="center" rowspan="1" colspan="1">0.143, 0.705</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"> Cluster North</td><td valign="top" align="center" rowspan="1" colspan="1">120</td><td valign="top" align="center" rowspan="1" colspan="1">71</td><td valign="top" align="center" rowspan="1" colspan="1">49</td><td valign="top" align="center" rowspan="1" colspan="1">4.033, 0.045*</td></tr><tr><td valign="top" align="left" scope="row" rowspan="1" colspan="1"><bold>Total</bold></td><td valign="top" align="center" rowspan="1" colspan="1">163</td><td valign="top" align="center" rowspan="1" colspan="1">86</td><td valign="top" align="center" rowspan="1" colspan="1">77</td><td valign="top" align="center" rowspan="1" colspan="1">0.497, 0.48</td></tr></tbody></table><table-wrap-foot><fn><p>MAT, mating type.</p></fn></table-wrap-foot></table-wrap></sec></sec><sec sec-type="discussion" id="s14"><title>Discussion</title><sec id="s15"><title>The <italic>MAT</italic> locus organization indicates heterothallism</title><p>All fungal species in this study are heterothallic because they have a locus with one of the two alternative single-copy idiomorphs, <italic>MAT1-1</italic> or <italic>MAT1-2</italic>. The organization of opposite <italic>MAT</italic> loci was highly conserved among <italic>L. longiclavatum</italic>, <italic>L. terebrantis</italic>, <italic>G. aurea</italic>, <italic>G. huntii</italic>, <italic>L. lundbergii</italic>, <italic>L. wingfieldii</italic>, and <italic>O. montium</italic>, thus supporting a common origin in Ophiostomatales (<xref rid="bib7" ref-type="bibr">Butler 2007</xref>). Also the general <italic>SLA-MAT-APN</italic> pattern, as well as the synteny and orientation of <italic>MAT1-1-1</italic>, <italic>MAT1-1-2</italic>, and <italic>MAT1-1-3</italic> genes on <italic>MAT1-1</italic> idiomorph are consistent with other representatives within Sordariomycetes, such as <italic>Neurospora</italic>, and <italic>Podospora</italic> (<xref rid="bib11" ref-type="bibr">Debuchy and Turgeon 2006</xref>). This suggests a common evolutionary origin of the <italic>MAT</italic> organization/structure for members of the Ophiostomatales and even the Sordariomycetes.</p><p>Whether heterothallism is the ancestral state in ascomycetes has been a major biological question in fungal evolution (<xref rid="bib9" ref-type="bibr">Coppin <italic>et al.</italic> 1997</xref>; <xref rid="bib7" ref-type="bibr">Butler 2007</xref>). Evolution from heterothallism (outcrossing) to homothallism (haploid selfing) could be the most likely scenario based on population genetics models (<xref rid="bib41" ref-type="bibr">Nauta and Hoekstra 1992</xref>; <xref rid="bib4" ref-type="bibr">Billiard <italic>et al.</italic> 2011</xref>). Recent analyses of mating-type evolution have ascertained <italic>Neurospora</italic> to be heterothallic in ancestry (<xref rid="bib60" ref-type="bibr">Strandberg <italic>et al.</italic> 2010</xref>; <xref rid="bib42" ref-type="bibr">Nygren <italic>et al.</italic> 2011</xref>; <xref rid="bib20" ref-type="bibr">Gioti <italic>et al.</italic> 2012</xref>). We speculate that the representative of <italic>Grosmannia</italic> and <italic>Ophiostoma</italic> may have diverged from the same common heterothallic ancestor as <italic>Neurospora</italic>. However, it is important to determine the mating-type organization from additional species in Ophiostomatales because their mating systems and breeding strategies (<xref rid="bib67" ref-type="bibr">Wilken <italic>et al.</italic> 2012</xref>) may be different from other Sordariomycetes.</p><p>Another special feature in the <italic>MAT</italic> locus is that <italic>COX13</italic> is located between <italic>MAT</italic> and <italic>APN</italic> genes in <italic>G. clavigera</italic>, and this is similar to the organization found in the human pathogen <italic>Histoplasma capsulatum</italic> (<xref rid="bib18" ref-type="bibr">Fraser <italic>et al.</italic> 2007</xref>). Although the <italic>MAT</italic> and <italic>APN</italic> loci were at least 15 kb apart, there was no evidence to suggest the presence of transposable elements, which have been reported in <italic>MAT</italic> locus expansion in the obligate biotroph <italic>Blumeria graminis</italic> (<xref rid="bib58" ref-type="bibr">Spanu <italic>et al.</italic> 2010</xref>), <italic>H. capsulatum</italic> (<xref rid="bib18" ref-type="bibr">Fraser <italic>et al.</italic> 2007</xref>) and the endophyte <italic>Phialocephala fortiniii</italic> (<xref rid="bib74" ref-type="bibr">Zaffarano <italic>et al.</italic> 2010</xref>).</p></sec><sec id="s16"><title>Unequal recombination defined the evolution of the truncated <italic>MAT1-1-1</italic> genes in <italic>Grosmannia</italic> and <italic>Ophiostoma</italic></title><p>Most fungi in this investigation carried the truncated <italic>MAT1-1-1</italic> in the <italic>MAT1-2</italic> idiomorphs. The polymorphism between full-length and truncated <italic>MAT1-1-1</italic> indicated that the event leading to the current <italic>MAT</italic> loci organization was ancient—before the radiation of <italic>G. clavigera</italic> from other species. A number of competing scenarios may account for the evolutionary origin of this unique organization.</p><p>Unequal recombination/crossover at the <italic>MAT</italic> locus between opposite mating-type idiomorphs during the pairing of chromosomes should be the most favorable mechanism to account for the truncated <italic>MAT1-1-1</italic> (<xref rid="bib20" ref-type="bibr">Gioti <italic>et al.</italic> 2012</xref>) (<xref ref-type="fig" rid="fig7">Figure 7</xref>). The ancestral <italic>MAT1-2</italic> idiomorph of <italic>Grosmannia</italic> and <italic>Ophiostoma</italic> members contained one ORF corresponding to the <italic>MAT1-2-1</italic> gene bearing the HMG domain. A fragment of the <italic>MAT1-1</italic> idiomorph, for instance the <italic>MAT1-1-1</italic> gene and the 5′end flanking sequence, could have become integrated into the ancestral <italic>MAT1-2</italic> idiomorph during the crossover in sexual reproduction (<xref ref-type="fig" rid="fig7">Figure 7</xref>). Afterward the α-box domain had been deleted over evolutionary time (<xref ref-type="fig" rid="fig7">Figure 7</xref>).</p><fig id="fig7" fig-type="figure" position="float"><label>Figure 7 </label><caption><p>Proposed model for the evolution of <italic>MAT</italic> locus in the common ancestor of <italic>Grosmannia</italic> and <italic>Ophiostoma</italic> (Ophiostomatales).</p></caption><graphic xlink:href="465f7"></graphic></fig><p>Unequal recombination at the <italic>MAT</italic> locus is not unique to members of <italic>Grosmannia</italic> and <italic>Ophiostoma</italic>. This event has clearly happened many times, and its footprints have been demonstrated in other ascomycete species (<xref rid="bib71" ref-type="bibr">Yokoyama <italic>et al.</italic> 2003</xref>; <xref rid="bib44" ref-type="bibr">Paoletti <italic>et al.</italic> 2005b</xref>; <xref rid="bib55" ref-type="bibr">Seidl <italic>et al.</italic> 2009</xref>; <xref rid="bib2" ref-type="bibr">Amselem <italic>et al.</italic> 2011</xref>; <xref rid="bib67" ref-type="bibr">Wilken <italic>et al.</italic> 2012</xref>) (<xref ref-type="fig" rid="fig5">Figure 5</xref>). Fragments of the <italic>MAT1-1-1</italic> and <italic>MAT1-1-3</italic> genes were reported in 10 isolates of <italic>O. quercus</italic> that contained the full, complete <italic>MAT1-2-1</italic> gene in their <italic>MAT1-2</italic> idiomorphs (<xref rid="bib67" ref-type="bibr">Wilken <italic>et al.</italic> 2012</xref>). Similarly, truncated <italic>MAT1-1-1</italic> genes were identified in the <italic>MAT1-2</italic> idiomorphs of at least five <italic>Phialocephala</italic> species (<xref rid="bib74" ref-type="bibr">Zaffarano <italic>et al.</italic> 2010</xref>) and the one in <italic>Hypocrea jecorina</italic> (<xref rid="bib55" ref-type="bibr">Seidl <italic>et al.</italic> 2009</xref>). In contrast, a partial <italic>MAT1-2-1</italic> sequence was found in the <italic>MAT1-1</italic> idiomorph of <italic>Aspergillus fumigatus</italic> (<xref rid="bib44" ref-type="bibr">Paoletti <italic>et al.</italic> 2005b</xref>). Also fragments of homologous <italic>MAT1-2-1</italic> and <italic>MAT1-1-1</italic> genes were detected bordering the mating-type idiomorphs in <italic>Botrytis cinerea</italic> isolates (<xref rid="bib2" ref-type="bibr">Amselem <italic>et al.</italic> 2011</xref>).</p><p>Recombination is supposed to be suppressed and rare at the <italic>MAT</italic> locus in ascomycetes (<xref rid="bib25" ref-type="bibr">Idnurm 2011</xref>), but recombination or crossover events have been reported. Homologs of <italic>MAT1-1-2</italic> and <italic>MAT1-1-3</italic> also were reported in the <italic>MAT1-2</italic> idiomorph of <italic>Diaporthe</italic> W- and G-type species, possibly due to recombination of idiomorphs (<xref rid="bib31" ref-type="bibr">Kanematsu <italic>et al.</italic> 2007</xref>). The <italic>MAT1-2-2</italic> gene in the <italic>MAT1-2</italic> idiomorph of <italic>Magnaporthe oryzae</italic> was partially homologous to the <italic>MAT1-1-3</italic> gene in opposite mating-types (<xref rid="bib30" ref-type="bibr">Kanamori <italic>et al.</italic> 2007</xref>). Recombination breakpoints and unequal crossover events have been revealed in the <italic>MAT</italic> loci of <italic>Neurospora</italic>, <italic>Cochliobolus</italic>, <italic>Stemphylium</italic>, <italic>Ascochyta</italic> and <italic>Phoma</italic> during the comparison of <italic>MAT</italic> idiomorphs between heterothallic to homothallic representatives (<xref rid="bib73" ref-type="bibr">Yun <italic>et al.</italic> 1999</xref>; <xref rid="bib26" ref-type="bibr">Inderbitzin <italic>et al.</italic> 2005</xref>; <xref rid="bib20" ref-type="bibr">Gioti <italic>et al.</italic> 2012</xref>; <xref rid="bib68" ref-type="bibr">Woudenberg <italic>et al.</italic> 2012</xref>).</p><p>Acquisition of <italic>MAT</italic> genes by transposition has been independently reported in several ascomycetes (<xref rid="bib53" ref-type="bibr">Rydholm <italic>et al.</italic> 2007</xref>; <xref rid="bib47" ref-type="bibr">Poggeler <italic>et al.</italic> 2011</xref>; <xref rid="bib20" ref-type="bibr">Gioti <italic>et al.</italic> 2012</xref>). Therefore, the intronless <italic>MAT1-1-1</italic> in <italic>MAT1-2</italic> idiomorph may have arisen by retrotransposition from the <italic>MAT1-1-1</italic> cDNA from the ancestral <italic>MAT1-1</italic> idiomorph, but the <italic>MAT</italic> loci do not contain transposon-related and repetitive sequences. Interspecific introgression of <italic>MAT1-1-1</italic> gene and vegetative incompatibility genes from <italic>Ophiostoma ulmi</italic> into <italic>O. novo-ulmi</italic> has been proposed (<xref rid="bib45" ref-type="bibr">Paoletti <italic>et al.</italic> 2006</xref>). Introgression or non-random acquisition of <italic>MAT</italic> genes was also demonstrated in the evolutionary histories among multiple <italic>Neurospora</italic> species (<xref rid="bib39" ref-type="bibr">Menkis <italic>et al.</italic> 2010</xref>; <xref rid="bib60" ref-type="bibr">Strandberg <italic>et al.</italic> 2010</xref>). However, the molecular data do not support introgression to account for the presence of the truncated <italic>MAT1-1-1</italic> gene because the gene genealogies of <italic>MAT</italic> and flanking genes do not contradict the species phylogeny of <italic>Grosmannia</italic> and <italic>Ophiostoma</italic> known from the housekeeping genes (<xref rid="bib36" ref-type="bibr">Lim <italic>et al.</italic> 2004</xref>), suggesting all these genes shared the same evolutionary history.</p><p>The occurrence of truncated mating-type genes in opposite <italic>MAT</italic> idiomorphs may suggest a common homothallic ancestor carrying a complete set of <italic>MAT</italic> genes, for instance all <italic>MAT1-1-1</italic>, <italic>MAT1-1-2</italic>, <italic>MAT1-1-3</italic>, and <italic>MAT1-2-1</italic> located at a single locus in the same order as <italic>Sordaria macrospora</italic> [Figure 15.2 in (<xref rid="bib11" ref-type="bibr">Debuchy and Turgeon 2006</xref>)]. The <italic>MAT1-1</italic> and <italic>MAT1-2</italic> idiomorphs could have arisen from the loss of HMG and α-box domain sequences as a result of multiple translocation breaks and segregations (<xref rid="bib44" ref-type="bibr">Paoletti <italic>et al.</italic> 2005b</xref>). This scenario had been proposed to explain the <italic>MAT</italic> locus evolution in <italic>Cordyceps takamontana</italic> (<xref rid="bib71" ref-type="bibr">Yokoyama <italic>et al.</italic> 2003</xref>), members of <italic>Botrytis</italic> and <italic>Sclerotinum</italic> (<xref rid="bib2" ref-type="bibr">Amselem <italic>et al.</italic> 2011</xref>), as well as the <italic>Aspergilli</italic> (<xref rid="bib19" ref-type="bibr">Galagan <italic>et al.</italic> 2005</xref>; <xref rid="bib44" ref-type="bibr">Paoletti <italic>et al.</italic> 2005b</xref>). However, this model of evolution is very unlikely based on the criterion of parsimony. Also <italic>G. clavigera</italic> and related fungi have syntenic order of <italic>MAT</italic> genes and may share a common heterothallic ancestor within the Sordariomycetes as discussed above.</p></sec><sec id="s17"><title>Deletion of the α-box domain due to evolutionary degeneration of <italic>MAT1-1-1</italic> genes</title><p>The deletion/removal of the α-box domain in the truncated <italic>MAT1-1-1</italic> gene may have been selected to avoid universal compatibility or haploid selfing (self-fertility) that involves no sexual recombination in reproduction (<xref rid="bib4" ref-type="bibr">Billiard <italic>et al.</italic> 2011</xref>, <xref rid="bib5" ref-type="bibr">2012</xref>). In fact, the expression of additional α-box domain may interfere or compete with the signal from the “resident/ original” HMG domain at the same locus (<xref rid="bib9" ref-type="bibr">Coppin <italic>et al.</italic> 1997</xref>), therefore the “additional” <italic>MAT1-1-1</italic> gene may have been “inactivated” for functions in mating (<xref rid="bib9" ref-type="bibr">Coppin <italic>et al.</italic> 1997</xref>) after the integration into the <italic>MAT</italic> locus as a result of unequal recombination. Under laboratory conditions, artificial association of both mating-type loci in the same nucleus of a heterothallic <italic>Neurospora crassa</italic> isolate led to inhibition of growth and the formation of barren perithecia in crosses with a tester (<xref rid="bib46" ref-type="bibr">Perkins 1972</xref>). Transgenic dual maters (carrying genes of both mating-types) were also unable to produce progeny in isolates of <italic>N. crassa</italic> (<xref rid="bib21" ref-type="bibr">Glass <italic>et al.</italic> 1990</xref>), <italic>Podospora anserina</italic> (<xref rid="bib10" ref-type="bibr">Coppin and Debuchy 2000</xref>) and <italic>Cochliobolus heterostrophus</italic> (<xref rid="bib66" ref-type="bibr">Turgeon <italic>et al.</italic> 1993</xref>).</p><p>In the absence of purifying selection, genes that have lost their original functions accumulate mutations and degenerate to become pseudogenes. Our data illustrated that the truncated <italic>MAT1-1-1</italic> gene in <italic>O. montium</italic> is highly eroded (31% in length compared with its ‘full length’ homolog) and could be a pseudogene. Similarly, the truncated <italic>MAT1-1-1</italic> gene reported in <italic>Cordyceps takamontana</italic> (known as <italic>Isaria tenuipes</italic>) was a pseudogene with accumulated mutations and stop codons (<xref rid="bib72" ref-type="bibr">Yokoyama <italic>et al.</italic> 2005</xref>). The 3′-end of the <italic>MAT1-1-1</italic> gene in the <italic>MAT1-2</italic> idiomorph of <italic>H. jecorina</italic> was also considered to be nonfunctional because the flanking region contained multiple stop codons with no translational start point detected (<xref rid="bib55" ref-type="bibr">Seidl <italic>et al.</italic> 2009</xref>). Also, the duplicated homeodomain transcription factors at <italic>A</italic> mating-type locus in <italic>Coprinopsis cinerea</italic> (Basidiomycota) were deleted and inactivated progressively (Kues <italic>et al.</italic> 2012). The <italic>MAT</italic> locus in yeasts was considered a “deletion hotspot” with a continued process of evolutionary deletions, gene truncation and transpositions on chromosomal genes located beside the <italic>MAT</italic> locus after the mating-type switching event (<xref rid="bib22" ref-type="bibr">Gordon <italic>et al.</italic> 2011</xref>).</p><p>The truncated <italic>MAT1-1-1</italic> genes in <italic>G. clavigera</italic> and relatives could have lost their original function in sexual reproduction but the degree of degeneration is not the same as the homolog in <italic>O. montium</italic>. However, these genes do not contain any stop codons and introns. The CODMEL tests indicated purifying selection at the inter-specific level due to accelerated rate of amino acid changes. The deletion of the α-box domain in the truncated <italic>MAT1-1-1</italic> genes also did not prevent its expression as it has already been demonstrated in <italic>Magnaporthe orzyae</italic> (<xref rid="bib30" ref-type="bibr">Kanamori <italic>et al.</italic> 2007</xref>). It is possible that the truncated genes have evolved new functions through adaptive evolution because the organization has been maintained in the entire phylogenetic clade. In contrast, the 3′-terminal truncated <italic>SXI1α</italic> gene at the <italic>MAT</italic> locus of <italic>Cryptococcus neoformans</italic> serotype-AD hybrid (Basidiomycota) is still functional in sexual reproduction and may even promote cell fusion (<xref rid="bib37" ref-type="bibr">Lin <italic>et al.</italic> 2007</xref>). Additional in-depth molecular genetics studies and experiments are necessary to elucidate the possible biological functions of the truncated <italic>MAT1-1-1</italic> gene.</p></sec><sec id="s18"><title>Implications for the mating strategies and breeding systems in fungi</title><p>Fungi within the Ophiostomatales have complex mating behavior that range from strict outcrossing (heterothallism) to haploid-selfing (homothallism) (<xref rid="bib23" ref-type="bibr">Gorton and Webber 2000</xref>; <xref rid="bib8" ref-type="bibr">Carlier <italic>et al.</italic> 2006</xref>). Also, <italic>Ophiostoma ulmi</italic> had been thought to perform ‘pseudoselfing’ by a process involved in mutation at the <italic>MAT</italic> locus or introgressed <italic>MAT</italic> genes that led to a mating-type switch (<xref rid="bib6" ref-type="bibr">Brasier and Gibbs 1975</xref>). Our results reflected that most members in <italic>Grosmannia</italic> are heterothallic in genetic makeup and they require a partner (outcrossing) to produce perithecia in life histories. These molecular data are largely congruent to the classical data from pairing-cultures, except that <italic>G. robusta</italic> was reported to produce perithecia readily in culture without pairing cultures (<xref rid="bib28" ref-type="bibr">Jacobs and Wingfield 2001</xref>). Also evidence of incongruence between molecular data and classical data were reported in <italic>O. quercus</italic>, as <italic>MAT1-2-1</italic> genes appeared to be present in both mating partners that are able to cross (<xref rid="bib67" ref-type="bibr">Wilken <italic>et al.</italic> 2012</xref>). Previous phylogenetic data demonstrated that homothallism has evolved multiple times independently from within heterothallic ascomycetes (<xref rid="bib73" ref-type="bibr">Yun <italic>et al.</italic> 1999</xref>; <xref rid="bib60" ref-type="bibr">Strandberg <italic>et al.</italic> 2010</xref>; <xref rid="bib4" ref-type="bibr">Billiard <italic>et al.</italic> 2011</xref>). Further characterization of the <italic>MAT</italic> loci from selfing species in Ophiostomatales based on classical mating studies could verify if homothallic members have been derived from a heterothallic ancestor, infer the phylogenetic relationships between the <italic>MAT</italic> locus organizations and reveal the mechanisms underlying the lifestyle changes.</p><p>Heterothallic (outcrossing) fungi gain benefits from recombination by increased genetic diversity and repaired mutation (<xref rid="bib24" ref-type="bibr">Heitman <italic>et al.</italic> 2007</xref>). The presence of both mating-type isolates in <italic>G. clavigera</italic> at different spatial scales is consistent with high levels of genotypic diversity found in this fungus (<xref rid="bib64" ref-type="bibr">Tsui <italic>et al.</italic> 2012</xref>). The finding of linkage equilibrium among microsatellite markers further indicated that sexual reproduction is a major factor influencing the population genetic structure and epidemiology of <italic>G. clavigera</italic> (<xref rid="bib64" ref-type="bibr">Tsui <italic>et al.</italic> 2012</xref>). If <italic>G. clavigera</italic> undergoes a sexual cycle regularly, the ascospores and ascomata should be discovered without difficulty. It was proposed that the inability to find the ascomata in nature is due to the inappropriate sampling methodology, or collecting plant material at the wrong stage in the life cycle (<xref rid="bib57" ref-type="bibr">Sommerhalder <italic>et al.</italic> 2006</xref>). Unfortunately, several attempts to cross complement isolates <italic>in vitro</italic> proved unsuccessful. Other possible explanations may be mutations in genes regulating the sexual development or environmental factors that reduce ascomata formation (<xref rid="bib3" ref-type="bibr">Bennett <italic>et al.</italic> 2003</xref>).</p><p>Finally, our results revealed the presence of homologous <italic>MAT</italic> genes in <italic>Llo</italic>, <italic>Lt</italic>, <italic>Lw</italic>, and <italic>Llun</italic>, which have long been considered to be asexual (<xref rid="bib28" ref-type="bibr">Jacobs and Wingfield 2001</xref>). We also found 1:1 mating-type ratio in <italic>L. longiclavatum</italic> populations. Evidence of purifying selection on the <italic>MAT</italic> genes at the inter-specific level indicated that sexual reproduction is important in nature or occurs regularly (<xref rid="bib38" ref-type="bibr">López-Villavicencio <italic>et al.</italic> 2010</xref>). Our data showed that these fungi previously deemed asexual have the potential to reproduce sexually, as was demonstrated for other asexual fungi such as <italic>Penicillium</italic>, <italic>Aspergillus</italic>, and <italic>Fusarium</italic> (<xref rid="bib7" ref-type="bibr">Butler 2007</xref>; <xref rid="bib51" ref-type="bibr">Ropars <italic>et al.</italic> 2012</xref>). This ability potentially increases genetic variability and can enhance fitness of fungal pathogens in new, ecological niches (<xref rid="bib9" ref-type="bibr">Coppin <italic>et al.</italic> 1997</xref>).</p></sec></sec><sec sec-type="supplementary-material"><title>Supplementary Material</title><supplementary-material id="PMC_1" content-type="local-data"><caption><title>Supporting Information</title></caption><media mimetype="text" mime-subtype="html" xlink:href="supp_3_3_465__index.html"></media><media xlink:role="associated-file" mimetype="application" mime-subtype="pdf" xlink:href="supp_3.3.465_004986SI.pdf"></media><media xlink:role="associated-file" mimetype="application" mime-subtype="pdf" xlink:href="supp_3.3.465_FigureS1.pdf"></media><media xlink:role="associated-file" mimetype="application" mime-subtype="pdf" xlink:href="supp_3.3.465_FigureS2.pdf"></media><media xlink:role="associated-file" mimetype="application" mime-subtype="pdf" xlink:href="supp_3.3.465_FigureS3.pdf"></media><media xlink:role="associated-file" mimetype="application" mime-subtype="pdf" xlink:href="supp_3.3.465_FigureS4.pdf"></media><media xlink:role="associated-file" mimetype="application" mime-subtype="pdf" xlink:href="supp_3.3.465_FigureS5.pdf"></media><media xlink:role="associated-file" mimetype="application" mime-subtype="pdf" xlink:href="supp_3.3.465_TableS2.pdf"></media><media xlink:role="associated-file" mimetype="application" mime-subtype="pdf" xlink:href="supp_3.3.465_TableS3.pdf"></media><media xlink:role="associated-file" mimetype="application" mime-subtype="pdf" xlink:href="supp_3.3.465_TableS4.pdf"></media><media xlink:role="associated-file" mimetype="application" mime-subtype="vnd.ms-excel" xlink:href="supp_3.3.465_TableS1.xls"></media></supplementary-material></sec></body><back><ack><title>Acknowledgments</title><p>We are grateful to the associate editor and the anonymous reviewers for their comments on the submitted manuscript. We acknowledge Paul Dyer and Carly Eagle (University of Nottingham, UK) for technical advice on the long-range PCR experiment; Tatiana Giraud, Evelyne Coppin, and Robert Debuchy (Université Paris-Sud, France); Colette Breuil, Jim Kronstad, and Mary Berbee (University of British Columbia, Canada) for advice and discussion on experimental design and data analyses. We are also grateful to Amanda Roe, Adrianne Rice, Felix Sperling, and Janice Cooke (University of Alberta, Canada) for providing additional cultures and DNA samples. We also thank Sepideh Alamouti, H.-J. Chen, Juan Valle, Ben Lai (UBC, Canada), and Forest Health Officers from the Alberta Sustainable Resource Development Fund for technical assistance, as well as Marc-André Rodrigue (Centre de recherche du CHUQ, Québec) for assistance in primer-walking sequencing. Financial assistance for this research was provided by Genome Canada, Genome British Columbia, Genome Alberta, and the Government of Alberta (AAET/AFRI-859-G07) in support of the Tria I and Tria II Projects <<ext-link ext-link-type="uri" xlink:href="http://www.thetriaproject.ca">http://www.thetriaproject.ca</ext-link>>, of which J.B. and R.C.H. are Principal Investigators. Funding was also provided by the Genomic Research and Development Initiative of Natural Resources Canada.</p></ack><fn-group><fn><p>Communicating editor: J. H. McCusker</p></fn></fn-group><ref-list><title>Literature Cited</title><ref id="bib1"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Alamouti</surname><given-names>S. M.</given-names></name><name><surname>Wang</surname><given-names>V.</given-names></name><name><surname>DiGuistini</surname><given-names>S.</given-names></name><name><surname>Six</surname><given-names>D.</given-names></name><name><surname>Bohlmann</surname><given-names>J.</given-names></name><etal></etal></person-group>, <year>2011</year> <article-title>Gene genealogies reveal cryptic species and host preferences for the pine fungal pathogen <italic>Grosmannia clavigera</italic></article-title>. <source>Mol. Ecol.</source><volume>12</volume>: <fpage>2581</fpage>–<lpage>2602</lpage><pub-id pub-id-type="pmid">21557782</pub-id></mixed-citation></ref><ref id="bib2"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Amselem</surname><given-names>J.</given-names></name><name><surname>Cuomo</surname><given-names>C. A.</given-names></name><name><surname>van Kan</surname><given-names>J. A.</given-names></name><name><surname>Viaud</surname><given-names>M.</given-names></name><name><surname>Benito</surname><given-names>E. P.</given-names></name><etal></etal></person-group>, <year>2011</year> <article-title>Genomic analysis of the necrotrophic fungal pathogens <italic>Sclerotinia sclerotiorum</italic> and <italic>Botrytis cinerea</italic></article-title>. <source>PLoS Genet.</source><volume>7</volume>: <fpage>e1002230</fpage><pub-id pub-id-type="pmid">21876677</pub-id></mixed-citation></ref><ref id="bib3"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bennett</surname><given-names>R. S.</given-names></name><name><surname>Yun</surname><given-names>S.</given-names></name><name><surname>Lee</surname><given-names>T. Y.</given-names></name><name><surname>Turgeon</surname><given-names>B. G.</given-names></name><name><surname>Arseniuk</surname><given-names>E.</given-names></name><etal></etal></person-group>, <year>2003</year> <article-title>Identity and conservation of mating type genes in geographically diverse isolates of <italic>Phaeosphaeria nodorum</italic></article-title>. <source>Fungal Genet. Biol.</source><volume>40</volume>: <fpage>25</fpage>–<lpage>37</lpage><pub-id pub-id-type="pmid">12948511</pub-id></mixed-citation></ref><ref id="bib4"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Billiard</surname><given-names>S.</given-names></name><name><surname>López-Villavicencio</surname><given-names>M.</given-names></name><name><surname>Devier</surname><given-names>B.</given-names></name><name><surname>Hood</surname><given-names>M. E.</given-names></name><name><surname>Fairhead</surname><given-names>C.</given-names></name><etal></etal></person-group>, <year>2011</year> <article-title>Having sex, yes, but with whom? Inferences from fungi on the evolution of anisogamy and mating types</article-title>. <source>Biol. Rev. Camb. Philos. Soc.</source><volume>86</volume>: <fpage>421</fpage>–<lpage>442</lpage><pub-id pub-id-type="pmid">21489122</pub-id></mixed-citation></ref><ref id="bib5"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Billiard</surname><given-names>S.</given-names></name><name><surname>Lopez-Villavicencio</surname><given-names>M.</given-names></name><name><surname>Hood</surname><given-names>M. E.</given-names></name><name><surname>Giraud</surname><given-names>T.</given-names></name></person-group>, <year>2012</year> <article-title>Sex, outcrossing and mating types: unsolved questions in fungi and beyond</article-title>. <source>J. Evol. Biol.</source><volume>25</volume>: <fpage>1020</fpage>–<lpage>1038</lpage><pub-id pub-id-type="pmid">22515640</pub-id></mixed-citation></ref><ref id="bib6"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Brasier</surname><given-names>C. M.</given-names></name><name><surname>Gibbs</surname><given-names>J. N.</given-names></name></person-group>, <year>1975</year> <article-title>Highly fertile form of the aggressive strain of <italic>Ceratocystis ulmi</italic></article-title>. <source>Nature</source><volume>257</volume>: <fpage>128</fpage>–<lpage>131</lpage></mixed-citation></ref><ref id="bib7"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Butler</surname><given-names>G.</given-names></name></person-group>, <year>2007</year> <article-title>The evolution of <italic>MAT</italic>: the ascomycetes</article-title>, pp. <fpage>3</fpage>–<lpage>18</lpage> in <source>Sex in Fungi: Molecular Determination and Evolutionary Implications</source>, edited by <person-group person-group-type="editor"><name><surname>Heitman</surname><given-names>J.</given-names></name><name><surname>Kronstad</surname><given-names>J. W.</given-names></name><name><surname>Taylor</surname><given-names>J. W.</given-names></name><name><surname>Casselton</surname><given-names>L. A.</given-names></name></person-group><publisher-name>ASM Press</publisher-name>, <publisher-loc>Washington, DC</publisher-loc></mixed-citation></ref><ref id="bib8"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Carlier</surname><given-names>F.-X.</given-names></name><name><surname>Decock</surname><given-names>C.</given-names></name><name><surname>Jacobs</surname><given-names>K.</given-names></name><name><surname>Maraite</surname><given-names>H.</given-names></name></person-group>, <year>2006</year> <article-title><italic>Ophiostoma arduennense</italic> sp. nov. (Ophiostomatales, Ascomycota) from <italic>Fagus sylvatica</italic> in southern Belgium</article-title>. <source>Mycol. Res.</source><volume>110</volume>: <fpage>801</fpage>–<lpage>810</lpage><pub-id pub-id-type="pmid">16828272</pub-id></mixed-citation></ref><ref id="bib9"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Coppin</surname><given-names>E.</given-names></name><name><surname>Debuchy</surname><given-names>R.</given-names></name><name><surname>Arnaise</surname><given-names>S.</given-names></name><name><surname>Picard</surname><given-names>M.</given-names></name></person-group>, <year>1997</year> <article-title>Mating types and sexual development in filamentous ascomycetes</article-title>. <source>Microbiol. Mol. Biol. Rev.</source><volume>61</volume>: <fpage>411</fpage>–<lpage>428</lpage><pub-id pub-id-type="pmid">9409146</pub-id></mixed-citation></ref><ref id="bib10"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Coppin</surname><given-names>E.</given-names></name><name><surname>Debuchy</surname><given-names>R.</given-names></name></person-group>, <year>2000</year> <article-title>Co-expression of the mating-type genes involved in internuclear recognition is lethal in <italic>Podospora anserina</italic></article-title>. <source>Genetics</source><volume>155</volume>: <fpage>657</fpage>–<lpage>669</lpage><pub-id pub-id-type="pmid">10835389</pub-id></mixed-citation></ref><ref id="bib11"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Debuchy</surname><given-names>R.</given-names></name><name><surname>Turgeon</surname><given-names>B. G.</given-names></name></person-group>, <year>2006</year> <article-title>Mating-type structure, function, and evolution in Euascomycetes</article-title>, pp. <fpage>293</fpage>–<lpage>323</lpage> in <source><italic>The Mycota I Growth</italic>, <italic>Differentiation</italic>, <italic>and Sexuality</italic></source>, edited by <person-group person-group-type="editor"><name><surname>Kües</surname><given-names>U.</given-names></name><name><surname>Fischer</surname><given-names>R.</given-names></name></person-group><publisher-name>Springer-Verlag</publisher-name>, <publisher-loc>Berlin, Heidelberg</publisher-loc></mixed-citation></ref><ref id="bib12"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Debuchy</surname><given-names>R.</given-names></name><name><surname>Berteaux-Lecellier</surname><given-names>V.</given-names></name><name><surname>Silar</surname><given-names>P.</given-names></name></person-group>, <year>2010</year> <article-title>Mating systems and sexual morphogenesis in ascomycetes</article-title>, pp. <fpage>501</fpage>–<lpage>535</lpage> in <source>Cellular and Molecular Biology of Filamentous Fungi</source>, edited by <person-group person-group-type="editor"><name><surname>Borkovich</surname><given-names>K. A.</given-names></name><name><surname>Ebbole</surname><given-names>D. J.</given-names></name></person-group><publisher-name>American Society for Microbiology Press</publisher-name>, <publisher-loc>Washington, DC</publisher-loc></mixed-citation></ref><ref id="bib13"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dereeper</surname><given-names>A.</given-names></name><name><surname>Guignon</surname><given-names>V.</given-names></name><name><surname>Blanc</surname><given-names>G.</given-names></name><name><surname>Audic</surname><given-names>S.</given-names></name><name><surname>Buffet</surname><given-names>S.</given-names></name><etal></etal></person-group>, <year>2008</year> <article-title>Phylogeny.fr: robust phylogenetic analysis for the non-specialist</article-title>. <source>Nucleic Acids Res.</source><volume>36</volume>: <fpage>W465–W469</fpage><pub-id pub-id-type="pmid">18424797</pub-id></mixed-citation></ref><ref id="bib14"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Devier</surname><given-names>B.</given-names></name><name><surname>Aguileta</surname><given-names>G.</given-names></name><name><surname>Hood</surname><given-names>M. E.</given-names></name><name><surname>Giraud</surname><given-names>T.</given-names></name></person-group>, <year>2009</year> <article-title>Ancient trans-specific polymorphism at pheromone receptor genes in Basidiomycetes</article-title>. <source>Genetics</source><volume>181</volume>: <fpage>209</fpage>–<lpage>223</lpage><pub-id pub-id-type="pmid">19001292</pub-id></mixed-citation></ref><ref id="bib15"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>DiGuistini</surname><given-names>S.</given-names></name><name><surname>Wang</surname><given-names>Y.</given-names></name><name><surname>Liao</surname><given-names>N. Y.</given-names></name><name><surname>Taylor</surname><given-names>G.</given-names></name><name><surname>Tanguay</surname><given-names>P.</given-names></name><etal></etal></person-group>, <year>2011</year> <article-title>Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont <italic>Grosmannia clavigera</italic></article-title>. <source>Proc. Natl. Acad. Sci. USA</source><volume>108</volume>: <fpage>2504</fpage>–<lpage>2509</lpage><pub-id pub-id-type="pmid">21262841</pub-id></mixed-citation></ref><ref id="bib16"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Farfan</surname><given-names>L.</given-names></name><name><surname>Tsui</surname><given-names>C. K. M.</given-names></name><name><surname>El-Kassaby</surname><given-names>Y. A.</given-names></name><name><surname>Hamelin</surname><given-names>R. C.</given-names></name></person-group>, <year>2011</year> <article-title>Population genetic analysis of <italic>Leptographium longiclavatum</italic> a pathogen associate with the mountain pine beetle <italic>Dendroctonus ponderosae</italic></article-title>. <source>Phytopathology</source><volume>101</volume>: <fpage>S51</fpage></mixed-citation></ref><ref id="bib17"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Felsenstein</surname><given-names>J.</given-names></name></person-group>, <year>2005</year> <source><italic>PHYLIP (Phylogeny Inference Package)</italic>, <italic>version 3.6a3</italic></source>. <publisher-name>Department of Genome Science. University of Washington</publisher-name>, <publisher-loc>Seattle, WA</publisher-loc></mixed-citation></ref><ref id="bib18"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Fraser</surname><given-names>J. A.</given-names></name><name><surname>Stajich</surname><given-names>J. E.</given-names></name><name><surname>Tarcha</surname><given-names>E. J.</given-names></name><name><surname>Cole</surname><given-names>G. T.</given-names></name><name><surname>Inglis</surname><given-names>D. O.</given-names></name><etal></etal></person-group>, <year>2007</year> <article-title>Evolution of the mating type locus: Insights gained from the dimorphic primary fungal pathogens <italic>Histoplasma capsulatum</italic>, <italic>Coccidioides immitis</italic>, and <italic>Coccidioides posadasii</italic></article-title>. <source>Eukaryot. Cell</source><volume>6</volume>: <fpage>622</fpage>–<lpage>629</lpage><pub-id pub-id-type="pmid">17337636</pub-id></mixed-citation></ref><ref id="bib19"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Galagan</surname><given-names>J. E.</given-names></name><name><surname>Calvo</surname><given-names>S. E.</given-names></name><name><surname>Cuomo</surname><given-names>C.</given-names></name><name><surname>Ma</surname><given-names>L. J.</given-names></name><name><surname>Wortman</surname><given-names>J. R.</given-names></name><etal></etal></person-group>, <year>2005</year> <article-title>Sequencing of <italic>Aspergillus nidulans</italic> and comparative analysis with <italic>A. fumigatus</italic> and <italic>A. oryzae</italic></article-title>. <source>Nature</source><volume>438</volume>: <fpage>1105</fpage>–<lpage>1115</lpage><pub-id pub-id-type="pmid">16372000</pub-id></mixed-citation></ref><ref id="bib20"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gioti</surname><given-names>A.</given-names></name><name><surname>Mushegian</surname><given-names>A. A.</given-names></name><name><surname>Strandberg</surname><given-names>R.</given-names></name><name><surname>Stajich</surname><given-names>J. E.</given-names></name><name><surname>Johannesson</surname><given-names>H.</given-names></name></person-group>, <year>2012</year> <article-title>Unidirectional evolutionary transitions in fungal mating systems and the role of transposable elements</article-title>. <source>Mol. Biol. Evol.</source><volume>29</volume>: <fpage>3215</fpage>–<lpage>3226</lpage><pub-id pub-id-type="pmid">22593224</pub-id></mixed-citation></ref><ref id="bib21"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Glass</surname><given-names>N. L.</given-names></name><name><surname>Grotelueschen</surname><given-names>J.</given-names></name><name><surname>Metzenberg</surname><given-names>R. L.</given-names></name></person-group>, <year>1990</year> <article-title><italic>Neurospora crassa</italic> A mating-type region</article-title>. <source>Proc. Natl. Acad. Sci. USA</source><volume>87</volume>: <fpage>4912</fpage>–<lpage>4916</lpage><pub-id pub-id-type="pmid">2142303</pub-id></mixed-citation></ref><ref id="bib22"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gordon</surname><given-names>J. L.</given-names></name><name><surname>Armisén</surname><given-names>D.</given-names></name><name><surname>Proux-Wéra</surname><given-names>E.</given-names></name><name><surname>Óhéigeartaigh</surname><given-names>S. S.</given-names></name><name><surname>Byrne</surname><given-names>K. P.</given-names></name><etal></etal></person-group>, <year>2011</year> <article-title>Evolutionary erosion of yeast sex chromosomes by mating-type switching accidents</article-title>. <source>Proc. Natl. Acad. Sci. USA</source><volume>108</volume>: <fpage>20024</fpage>–<lpage>20029</lpage><pub-id pub-id-type="pmid">22123960</pub-id></mixed-citation></ref><ref id="bib23"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gorton</surname><given-names>C.</given-names></name><name><surname>Webber</surname><given-names>J. F.</given-names></name></person-group>, <year>2000</year> <article-title>Reevaluation of the status of the bluestain fungus and bark beetle associate <italic>Ophiostoma minus</italic></article-title>. <source>Mycologia</source><volume>92</volume>: <fpage>1071</fpage>–<lpage>1079</lpage></mixed-citation></ref><ref id="bib24"><mixed-citation publication-type="book"><person-group person-group-type="editor"><name><surname>J.</surname><given-names>Heitman</given-names></name><name><surname>Kronstad</surname><given-names>J. W.</given-names></name><name><surname>Taylor</surname><given-names>J. W.</given-names></name><name><surname>Casselton</surname><given-names>L. A.</given-names></name></person-group> (Editors), <year>2007</year> <source>Sex in Fungi: Molecular Determination and Evolutionary Implications</source>. <publisher-name>ASM Press</publisher-name>, <publisher-loc>Washington, DC</publisher-loc></mixed-citation></ref><ref id="bib25"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Idnurm</surname><given-names>A.</given-names></name></person-group>, <year>2011</year> <article-title>Sex and speciation: The paradox that non-recombining DNA promotes recombination</article-title>. <source>Fungal Biol. Rev.</source><volume>25</volume>: <fpage>121</fpage>–<lpage>127</lpage><pub-id pub-id-type="pmid">23136582</pub-id></mixed-citation></ref><ref id="bib26"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Inderbitzin</surname><given-names>P.</given-names></name><name><surname>Harkness</surname><given-names>J.</given-names></name><name><surname>Turgeon</surname><given-names>B. G.</given-names></name><name><surname>Berbee</surname><given-names>M. L.</given-names></name></person-group>, <year>2005</year> <article-title>Lateral transfer of mating system in <italic>Stemphylium</italic></article-title>. <source>Proc. Natl. Acad. Sci. USA</source><volume>102</volume>: <fpage>11390</fpage>–<lpage>11395</lpage><pub-id pub-id-type="pmid">16055562</pub-id></mixed-citation></ref><ref id="bib27"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jacobi</surname><given-names>V.</given-names></name><name><surname>Dufour</surname><given-names>J.</given-names></name><name><surname>Bouvet</surname><given-names>G. F.</given-names></name><name><surname>Aoun</surname><given-names>M.</given-names></name><name><surname>Bernier</surname><given-names>L.</given-names></name></person-group>, <year>2010</year> <article-title>Identification of transcripts up-regulated in asexual and sexual fruiting bodies of the Dutch elm disease pathogen <italic>Ophiostoma novo-ulmi</italic></article-title>. <source>Can. J. Microbiol.</source><volume>58</volume>: <fpage>697</fpage>–<lpage>705</lpage><pub-id pub-id-type="pmid">20725133</pub-id></mixed-citation></ref><ref id="bib28"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Jacobs</surname><given-names>K.</given-names></name><name><surname>Wingfield</surname><given-names>M. J.</given-names></name></person-group>, <year>2001</year> <source><italic>Leptographium Species: Tree Pathogens</italic>, <italic>Insect Associates</italic>, <italic>and Agents of Blue-Stain</italic></source>. <publisher-name>American Phytopathological Society Press</publisher-name>, <publisher-loc>St. Paul, MN</publisher-loc></mixed-citation></ref><ref id="bib29"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Joly</surname><given-names>D. L.</given-names></name><name><surname>Feau</surname><given-names>N.</given-names></name><name><surname>Tanguay</surname><given-names>P.</given-names></name><name><surname>Hamelin</surname><given-names>R. C.</given-names></name></person-group>, <year>2010</year> <article-title>Comparative analysis of secreted protein evolution using expressed sequence tags from four poplar leaf rusts (<italic>Melampsora</italic> spp. )</article-title>. <source>BMC Genomics</source><volume>11</volume>: <fpage>422</fpage><pub-id pub-id-type="pmid">20615251</pub-id></mixed-citation></ref><ref id="bib30"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kanamori</surname><given-names>M.</given-names></name><name><surname>Kato</surname><given-names>H.</given-names></name><name><surname>Yasuda</surname><given-names>N.</given-names></name><name><surname>Koizumi</surname><given-names>S.</given-names></name><name><surname>Peever</surname><given-names>T. L.</given-names></name><etal></etal></person-group>, <year>2007</year> <article-title>Novel mating type-dependent transcripts at the mating type locus in <italic>Magnaporthe oryzae</italic></article-title>. <source>Gene</source><volume>403</volume>: <fpage>6</fpage>–<lpage>17</lpage><pub-id pub-id-type="pmid">17881155</pub-id></mixed-citation></ref><ref id="bib31"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kanematsu</surname><given-names>S.</given-names></name><name><surname>Adachi</surname><given-names>Y.</given-names></name><name><surname>Ito</surname><given-names>T.</given-names></name></person-group>, <year>2007</year> <article-title>Mating-type loci of heterothallic <italic>Diaporthe</italic> spp.: homologous genes are present in opposite mating-types</article-title>. <source>Curr. Genet.</source><volume>52</volume>: <fpage>11</fpage>–<lpage>22</lpage><pub-id pub-id-type="pmid">17476509</pub-id></mixed-citation></ref><ref id="bib32"><mixed-citation publication-type="confproc"><person-group person-group-type="author"><name><surname>Kües</surname><given-names>U.</given-names></name><name><surname>Yu</surname><given-names>Y.-D.</given-names></name><name><surname>Navarro-Gonzalez</surname><given-names>M.</given-names></name></person-group>, <year>2012</year> <article-title>A mating loci in Coprinopsis cinerea differ in numbers of homeodomain transcription factor genes</article-title>, p. 37 in <source>Abstract Book of 11th European Conference on Fungal Genetics</source>, <publisher-loc>Marburg, Germany</publisher-loc></mixed-citation></ref><ref id="bib33"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kurz</surname><given-names>W. A.</given-names></name><name><surname>Dymond</surname><given-names>C. C.</given-names></name><name><surname>Stinson</surname><given-names>G.</given-names></name><name><surname>Rampley</surname><given-names>G. J.</given-names></name><name><surname>Neilson</surname><given-names>E. T.</given-names></name><etal></etal></person-group>, <year>2008</year> <article-title>Mountain pine beetle and forest carbon feedback to climate change</article-title>. <source>Nature</source><volume>452</volume>: <fpage>987</fpage>–<lpage>990</lpage><pub-id pub-id-type="pmid">18432244</pub-id></mixed-citation></ref><ref id="bib34"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lee</surname><given-names>S.</given-names></name><name><surname>Kim</surname><given-names>J.</given-names></name><name><surname>Breuil</surname><given-names>C.</given-names></name></person-group>, <year>2005</year> <article-title><italic>Leptographium longiclavatum</italic> sp. nov., a new species associated with the mountain pine beetle, <italic>Dendroctonus ponderosae</italic></article-title>. <source>Mycol. Res.</source><volume>109</volume>: <fpage>1162</fpage>–<lpage>1170</lpage><pub-id pub-id-type="pmid">16279410</pub-id></mixed-citation></ref><ref id="bib35"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lee</surname><given-names>S.</given-names></name><name><surname>Hamelin</surname><given-names>R. C.</given-names></name><name><surname>Six</surname><given-names>D. L.</given-names></name><name><surname>Breuil</surname><given-names>C.</given-names></name></person-group>, <year>2007</year> <article-title>Genetic diversity and the presence of two distinct groups in <italic>Ophiostoma clavigerum</italic> associated with <italic>Dendroctonus ponderosae</italic> in British Columbia and the Northern Rocky Mountains</article-title>. <source>Phytopathology</source><volume>97</volume>: <fpage>1177</fpage>–<lpage>1185</lpage><pub-id pub-id-type="pmid">18944182</pub-id></mixed-citation></ref><ref id="bib36"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lim</surname><given-names>Y. W.</given-names></name><name><surname>Alamouti</surname><given-names>S. M.</given-names></name><name><surname>Kim</surname><given-names>J.</given-names></name><name><surname>Lee</surname><given-names>S.</given-names></name><name><surname>Breuil</surname><given-names>C.</given-names></name></person-group>, <year>2004</year> <article-title>Multigene phylogenies of <italic>Ophiostoma clavigerum</italic> and closely related species from bark beetle-attacked <italic>Pinus</italic> in North America</article-title>. <source>FEMS Microbiol. Lett.</source><volume>237</volume>: <fpage>89</fpage>–<lpage>96</lpage><pub-id pub-id-type="pmid">15268942</pub-id></mixed-citation></ref><ref id="bib37"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lin</surname><given-names>X.</given-names></name><name><surname>Litvintseva</surname><given-names>A. P.</given-names></name><name><surname>Nielsen</surname><given-names>K.</given-names></name><name><surname>Patel</surname><given-names>S.</given-names></name><name><surname>Floyd</surname><given-names>A.</given-names></name><etal></etal></person-group>, <year>2007</year> <article-title>alpha AD alpha hybrids of <italic>Cryptococcus neoformans</italic>: evidence of same-sex mating in nature and hybrid fitness</article-title>. <source>PLoS Genet.</source><volume>3</volume>: <fpage>1975</fpage>–<lpage>1990</lpage><pub-id pub-id-type="pmid">17953489</pub-id></mixed-citation></ref><ref id="bib38"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>López-Villavicencio</surname><given-names>M.</given-names></name><name><surname>Aguileta</surname><given-names>G.</given-names></name><name><surname>Giraud</surname><given-names>T.</given-names></name><name><surname>de Vienne</surname><given-names>D. M.</given-names></name><name><surname>Lacoste</surname><given-names>S.</given-names></name><etal></etal></person-group>, <year>2010</year> <article-title>Sex in <italic>Penicillium</italic>: Combined phylogenetic and experimental approaches</article-title>. <source>Fungal Genet. Biol.</source><volume>47</volume>: <fpage>693</fpage>–<lpage>706</lpage><pub-id pub-id-type="pmid">20460164</pub-id></mixed-citation></ref><ref id="bib39"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Menkis</surname><given-names>A.</given-names></name><name><surname>Whittle</surname><given-names>C. A.</given-names></name><name><surname>Johannesson</surname><given-names>H.</given-names></name></person-group>, <year>2010</year> <article-title>Gene genealogies indicate abundant gene conversions and independent evolutionary histories of the mating-type chromosomes in the evolutionary history of <italic>Neurospora tetrasperma</italic></article-title>. <source>BMC Evol. Biol.</source><volume>10</volume>: <fpage>234</fpage><pub-id pub-id-type="pmid">20673371</pub-id></mixed-citation></ref><ref id="bib40"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Metzenberg</surname><given-names>R. L.</given-names></name><name><surname>Glass</surname><given-names>N. L.</given-names></name></person-group>, <year>1990</year> <article-title>Mating type and mating strategies in <italic>Neurospora</italic></article-title>. <source>Bioessays</source><volume>12</volume>: <fpage>53</fpage>–<lpage>59</lpage><pub-id pub-id-type="pmid">2140508</pub-id></mixed-citation></ref><ref id="bib41"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nauta</surname><given-names>M. J.</given-names></name><name><surname>Hoekstra</surname><given-names>H. F.</given-names></name></person-group>, <year>1992</year> <article-title>Evolution of reproductive systems in filamentous ascomycetes. I. Evolution of mating types</article-title>. <source>Evolution</source><volume>68</volume>: <fpage>405</fpage>–<lpage>410</lpage></mixed-citation></ref><ref id="bib42"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nygren</surname><given-names>K.</given-names></name><name><surname>Strandberg</surname><given-names>R.</given-names></name><name><surname>Wallberg</surname><given-names>A.</given-names></name><name><surname>Nabholz</surname><given-names>B.</given-names></name><name><surname>Gustafsson</surname><given-names>T.</given-names></name><etal></etal></person-group>, <year>2011</year> <article-title>A comprehensive phylogeny of <italic>Neurospora</italic> reveals a link between reproductive mode and molecular evolution in fungi</article-title>. <source>Mol. Phylogenet. Evol.</source><volume>59</volume>: <fpage>649</fpage>–<lpage>663</lpage><pub-id pub-id-type="pmid">21439389</pub-id></mixed-citation></ref><ref id="bib43"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Paoletti</surname><given-names>M.</given-names></name><name><surname>Buck</surname><given-names>K. W.</given-names></name><name><surname>Brasier</surname><given-names>C. M.</given-names></name></person-group>, <year>2005</year><comment>a</comment> <article-title>Cloning and sequence analysis of the <italic>MAT-B</italic> (<italic>MAT-2</italic>) genes from the three Dutch elm disease pathogens, <italic>Ophiostoma ulmi</italic></article-title>. <source>Mycol. Res.</source><volume>109</volume>: <fpage>983</fpage>–<lpage>991</lpage><pub-id pub-id-type="pmid">16209304</pub-id></mixed-citation></ref><ref id="bib44"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Paoletti</surname><given-names>M.</given-names></name><name><surname>Rydholm</surname><given-names>C.</given-names></name><name><surname>Schwier</surname><given-names>E. U.</given-names></name><name><surname>Anderson</surname><given-names>M. J.</given-names></name><name><surname>Szakacs</surname><given-names>G.</given-names></name><etal></etal></person-group>, <year>2005</year><comment>b</comment> <article-title>Evidence for sexuality in the opportunistic fungal pathogen <italic>Aspergillus fumigatus</italic></article-title>. <source>Curr. Biol.</source><volume>15</volume>: <fpage>1242</fpage>–<lpage>1248</lpage><pub-id pub-id-type="pmid">16005299</pub-id></mixed-citation></ref><ref id="bib45"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Paoletti</surname><given-names>M.</given-names></name><name><surname>Buck</surname><given-names>K. W.</given-names></name><name><surname>Brasier</surname><given-names>C. M.</given-names></name></person-group>, <year>2006</year> <article-title>Selective acquisition of novel mating type and vegetative incompatibility genes via interspecies gene transfer in the globally invading eukaryote <italic>Ophiostoma novo-ulmi</italic></article-title>. <source>Mol. Ecol.</source><volume>15</volume>: <fpage>249</fpage>–<lpage>262</lpage><pub-id pub-id-type="pmid">16367844</pub-id></mixed-citation></ref><ref id="bib46"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Perkins</surname><given-names>D. D.</given-names></name></person-group>, <year>1972</year> <article-title>An insertional translocation in <italic>Neurospora</italic> that generates duplications heterozygous for mating type</article-title>. <source>Genetics</source><volume>71</volume>: <fpage>25</fpage>–<lpage>51</lpage><pub-id pub-id-type="pmid">17248574</pub-id></mixed-citation></ref><ref id="bib47"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Poggeler</surname><given-names>S.</given-names></name><name><surname>O’Gorman</surname><given-names>C. M.</given-names></name><name><surname>Hoff</surname><given-names>B.</given-names></name><name><surname>Kuck</surname><given-names>U.</given-names></name></person-group>, <year>2011</year> <article-title>Molecular organization of the mating-type loci in the homothallic Ascomycete <italic>Eupenicillium crustaceum</italic></article-title>. <source>Fungal Biol.</source><volume>115</volume>: <fpage>615</fpage>–<lpage>624</lpage><pub-id pub-id-type="pmid">21724167</pub-id></mixed-citation></ref><ref id="bib48"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Posada</surname><given-names>D.</given-names></name></person-group>, <year>2006</year> <article-title>ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online</article-title>. <source>Nucleic Acids Res.</source><volume>34</volume>: <fpage>W700–S703</fpage><pub-id pub-id-type="pmid">16845102</pub-id></mixed-citation></ref><ref id="bib49"><mixed-citation publication-type="webpage">Rambaut, A., 1999 Se-Al: Sequence Alignment Editor. Available at: <<ext-link ext-link-type="uri" xlink:href="http://evolve.zoo.ox.ac.uk/">http://evolve.zoo.ox.ac.uk/</ext-link>>. Accessed: January 15, 2013.</mixed-citation></ref><ref id="bib50"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Roe</surname><given-names>A.</given-names></name><name><surname>Rice</surname><given-names>S. V.</given-names></name><name><surname>Coltman</surname><given-names>D. W.</given-names></name><name><surname>Cooke</surname><given-names>J. E. K.</given-names></name><name><surname>Sperling</surname><given-names>F. A. H.</given-names></name></person-group>, <year>2011</year> <article-title>Comparative phylogeography, genetic differentiation and contrasting reproductive modes in three fungal symbionts of a multipartite bark beetle symbiosis</article-title>. <source>Mol. Ecol.</source><volume>20</volume>: <fpage>584</fpage>–<lpage>600</lpage><pub-id pub-id-type="pmid">21166729</pub-id></mixed-citation></ref><ref id="bib51"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ropars</surname><given-names>J.</given-names></name><name><surname>Dupont</surname><given-names>J.</given-names></name><name><surname>Fontanillas</surname><given-names>E.</given-names></name><name><surname>Rodríguez de la Vega</surname><given-names>R. C.</given-names></name><name><surname>Malagnac</surname><given-names>F.</given-names></name><etal></etal></person-group>, <year>2012</year> <article-title>Sex in cheese: evidence for sexuality in the fungus <italic>Penicillium roqueforti</italic></article-title>. <source>PLoS ONE</source><volume>7</volume>: <fpage>e49665</fpage><pub-id pub-id-type="pmid">23185400</pub-id></mixed-citation></ref><ref id="bib52"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rutherford</surname><given-names>K.</given-names></name><name><surname>Parkhil</surname><given-names>J.</given-names></name><name><surname>Crook</surname><given-names>J.</given-names></name><name><surname>Horsnell</surname><given-names>T.</given-names></name><name><surname>Rice</surname><given-names>P.</given-names></name></person-group>, <year>2000</year> <article-title>Artemis: sequence visualization and annotation</article-title>. <source>Bioinformatics</source><volume>16</volume>: <fpage>944</fpage>–<lpage>945</lpage><pub-id pub-id-type="pmid">11120685</pub-id></mixed-citation></ref><ref id="bib53"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rydholm</surname><given-names>C.</given-names></name><name><surname>Dyer</surname><given-names>P. S.</given-names></name><name><surname>Lutzoni</surname><given-names>F.</given-names></name></person-group>, <year>2007</year> <article-title>DNA sequence characterization and molecular evolution of <italic>MAT1</italic> and <italic>MAT2</italic> mating-type loci of the self-compatible ascomycete mold <italic>Neosartorya fischeri</italic></article-title>. <source>Eukaryot. Cell</source><volume>6</volume>: <fpage>868</fpage>–<lpage>874</lpage><pub-id pub-id-type="pmid">17384199</pub-id></mixed-citation></ref><ref id="bib54"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Safranyik</surname><given-names>L.</given-names></name><name><surname>Carroll</surname><given-names>A. L.</given-names></name><name><surname>Régnière</surname><given-names>J.</given-names></name><name><surname>Langor</surname><given-names>D. W.</given-names></name><name><surname>Riel</surname><given-names>W. G.</given-names></name><etal></etal></person-group>, <year>2010</year><article-title>Potential for range expansion of mountain pine beetle into the boreal forest of North America</article-title>. <source>Canadian Entomologist</source><volume>142</volume>: <fpage>415</fpage>–<lpage>442</lpage></mixed-citation></ref><ref id="bib55"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Seidl</surname><given-names>V.</given-names></name><name><surname>Seibel</surname><given-names>C.</given-names></name><name><surname>Kubicek</surname><given-names>C. P.</given-names></name><name><surname>Schmoll</surname><given-names>M.</given-names></name></person-group>, <year>2009</year> <article-title>Sexual development in the industrial workhorse <italic>Trichoderma reesei</italic></article-title>. <source>Proc. Natl. Acad. Sci. USA</source><volume>106</volume>: <fpage>13909</fpage>–<lpage>13914</lpage><pub-id pub-id-type="pmid">19667182</pub-id></mixed-citation></ref><ref id="bib56"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Solheim</surname><given-names>H.</given-names></name><name><surname>Krokene</surname><given-names>P.</given-names></name></person-group>, <year>1998</year> <article-title>Growth and virulence of mountain pine beetle associated blue-stain fungi, <italic>Ophiostoma clavigerum</italic> and <italic>Ophiostoma montium</italic></article-title>. <source>Can. J. Bot.</source><volume>76</volume>: <fpage>561</fpage>–<lpage>566</lpage></mixed-citation></ref><ref id="bib57"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sommerhalder</surname><given-names>R. J.</given-names></name><name><surname>Mcdonald</surname><given-names>B. A.</given-names></name><name><surname>Zhan</surname><given-names>J.</given-names></name></person-group>, <year>2006</year> <article-title>The frequencies and spatial distribution of mating types in <italic>Stagonospora nodorum</italic> are consistent with recurring sexual reproduction</article-title>. <source>Phytopathology</source><volume>96</volume>: <fpage>234</fpage>–<lpage>239</lpage><pub-id pub-id-type="pmid">18944437</pub-id></mixed-citation></ref><ref id="bib58"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Spanu</surname><given-names>P. D.</given-names></name><name><surname>Abbott</surname><given-names>J. C.</given-names></name><name><surname>Amselem</surname><given-names>J.</given-names></name><name><surname>Burgis</surname><given-names>T. A.</given-names></name><name><surname>Soanes</surname><given-names>D. M.</given-names></name><etal></etal></person-group>, <year>2010</year> <article-title>Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism</article-title>. <source>Science</source><volume>330</volume>: <fpage>1543</fpage>–<lpage>1546</lpage><pub-id pub-id-type="pmid">21148392</pub-id></mixed-citation></ref><ref id="bib59"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Staden</surname><given-names>R.</given-names></name></person-group>, <year>1996</year> <article-title>The Staden sequence analysis package</article-title>. <source>Mol. Biotechnol.</source><volume>5</volume>: <fpage>233</fpage>–<lpage>241</lpage><pub-id pub-id-type="pmid">8837029</pub-id></mixed-citation></ref><ref id="bib60"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Strandberg</surname><given-names>R.</given-names></name><name><surname>Nygren</surname><given-names>K.</given-names></name><name><surname>Menkis</surname><given-names>A.</given-names></name><name><surname>James</surname><given-names>T. Y.</given-names></name><name><surname>Wik</surname><given-names>L.</given-names></name><name><surname>Stajich</surname><given-names>J. E.</given-names></name><etal></etal></person-group>, <year>2010</year> <article-title>Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus <italic>Neurospora</italic></article-title>. <source>Fungal Genet. Biol.</source><volume>47</volume>: <fpage>869</fpage>–<lpage>878</lpage><pub-id pub-id-type="pmid">20601044</pub-id></mixed-citation></ref><ref id="bib61"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Swofford</surname><given-names>D. L.</given-names></name></person-group>, <year>2003</year> <source>PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods)</source>. <publisher-name>Sinauer Associates</publisher-name>, <publisher-loc>Sunderland, MA</publisher-loc></mixed-citation></ref><ref id="bib62"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Tamura</surname><given-names>K.</given-names></name><name><surname>Peterson</surname><given-names>D.</given-names></name><name><surname>Peterson</surname><given-names>N.</given-names></name><name><surname>Stecher</surname><given-names>G.</given-names></name><name><surname>Nei</surname><given-names>M.</given-names></name><etal></etal></person-group>, <year>2011</year> <article-title>MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods</article-title>. <source>Mol. Biol. Evol.</source><volume>28</volume>: <fpage>2731</fpage>–<lpage>2739</lpage><pub-id pub-id-type="pmid">21546353</pub-id></mixed-citation></ref><ref id="bib63"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Thompson</surname><given-names>J. D.</given-names></name><name><surname>Gibson</surname><given-names>T. J.</given-names></name><name><surname>Plewniak</surname><given-names>F.</given-names></name><name><surname>Jeanmougin</surname><given-names>F.</given-names></name><name><surname>Higgins</surname><given-names>D. G.</given-names></name></person-group>, <year>1997</year> <article-title>The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools</article-title>. <source>Nucleic Acids Res.</source><volume>25</volume>: <fpage>4876</fpage>–<lpage>4882</lpage><pub-id pub-id-type="pmid">9396791</pub-id></mixed-citation></ref><ref id="bib64"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Tsui</surname><given-names>C. K. M.</given-names></name><name><surname>Roe</surname><given-names>A. D.</given-names></name><name><surname>El-Kassaby</surname><given-names>Y. A.</given-names></name><name><surname>Rice</surname><given-names>A. V.</given-names></name><name><surname>Alamounti</surname><given-names>S. M.</given-names></name><etal></etal></person-group>, <year>2012</year> <article-title>Population structure and migration pattern of a conifer pathogen, <italic>Grosmannia clavigera</italic>, as influenced by its symbiont, the mountain pine beetle</article-title>. <source>Mol. Ecol.</source><volume>21</volume>: <fpage>71</fpage>–<lpage>86</lpage><pub-id pub-id-type="pmid">22118059</pub-id></mixed-citation></ref><ref id="bib65"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Turgeon</surname><given-names>B. G.</given-names></name><name><surname>Yoder</surname><given-names>O. C.</given-names></name></person-group>, <year>2000</year> <article-title>Proposed nomenclature for Mating type genes of filamentous ascomycetes</article-title>. <source>Fungal Genet. Biol.</source><volume>31</volume>: <fpage>1</fpage>–<lpage>5</lpage><pub-id pub-id-type="pmid">11118130</pub-id></mixed-citation></ref><ref id="bib66"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Turgeon</surname><given-names>B. G.</given-names></name><name><surname>Bohlmann</surname><given-names>H.</given-names></name><name><surname>Ciuffetti</surname><given-names>L. M.</given-names></name><name><surname>Christiansen</surname><given-names>S. K.</given-names></name><name><surname>Yang</surname><given-names>G.</given-names></name><etal></etal></person-group>, <year>1993</year> <article-title>Cloning and analysis of the mating type genes from <italic>Cochliobolus heterostrophus</italic></article-title>. <source>Mol. Gen. Genet.</source><volume>238</volume>: <fpage>270</fpage>–<lpage>284</lpage><pub-id pub-id-type="pmid">8479433</pub-id></mixed-citation></ref><ref id="bib67"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wilken</surname><given-names>P. M.</given-names></name><name><surname>Steenkamp</surname><given-names>E. T.</given-names></name><name><surname>Hall</surname><given-names>T. A.</given-names></name><name><surname>de Beer</surname><given-names>Z. W.</given-names></name><name><surname>Wingfield</surname><given-names>M. J.</given-names></name><etal></etal></person-group>, <year>2012</year> <article-title>Both mating types in the heterothallic fungus <italic>Ophiostoma quercus</italic> contain <italic>MAT1–1</italic> and <italic>MAT1–2</italic> genes</article-title>. <source>Fungal Biol.</source><volume>116</volume>: <fpage>427</fpage>–<lpage>437</lpage><pub-id pub-id-type="pmid">22385624</pub-id></mixed-citation></ref><ref id="bib68"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Woudenberg</surname><given-names>J. H. C.</given-names></name><name><surname>de Gruyter</surname><given-names>J.</given-names></name><name><surname>Crous</surname><given-names>P. W.</given-names></name><name><surname>Zwiers</surname><given-names>L. H.</given-names></name></person-group>, <year>2012</year> <article-title>Analysis of the mating-type loci of co-occurring and phylogenetically related species of <italic>Ascochyta</italic> and <italic>Phoma</italic></article-title>. <source>Mol. Plant Pathol.</source><volume>13</volume>: <fpage>350</fpage>–<lpage>362</lpage><pub-id pub-id-type="pmid">22014305</pub-id></mixed-citation></ref><ref id="bib69"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yamaoka</surname><given-names>Y.</given-names></name><name><surname>Hiratsuka</surname><given-names>Y.</given-names></name><name><surname>Maruyama</surname><given-names>P. J.</given-names></name></person-group>, <year>1995</year> <article-title>The ability of <italic>Ophiostoma clavigerum</italic> to kill mature lodgepole-pine trees</article-title>. <source>Eur. J. Forest Pathol.</source><volume>25</volume>: <fpage>401</fpage>–<lpage>404</lpage></mixed-citation></ref><ref id="bib70"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yang</surname><given-names>Z.</given-names></name></person-group>, <year>2007</year> <article-title>PAML 4: phylogenetic analysis by maximum likelihood</article-title>. <source>Mol. Biol. Evol.</source><volume>24</volume>: <fpage>1586</fpage>–<lpage>1591</lpage><pub-id pub-id-type="pmid">17483113</pub-id></mixed-citation></ref><ref id="bib71"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yokoyama</surname><given-names>E.</given-names></name><name><surname>Yamagishi</surname><given-names>K.</given-names></name><name><surname>Hara</surname><given-names>A.</given-names></name><name><surname>Yokoyama</surname><given-names>E.</given-names></name><name><surname>Yamagishi</surname><given-names>K.</given-names></name><etal></etal></person-group>, <year>2003</year> <article-title>Structures of the mating-type loci of <italic>Cordyceps takaomontana</italic></article-title>. <source>Appl. Environ. Microbiol.</source><volume>69</volume>: <fpage>5019</fpage>–<lpage>5022</lpage><pub-id pub-id-type="pmid">12902305</pub-id></mixed-citation></ref><ref id="bib72"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yokoyama</surname><given-names>E.</given-names></name><name><surname>Yamagishi</surname><given-names>K.</given-names></name><name><surname>Hara</surname><given-names>A.</given-names></name></person-group>, <year>2005</year> <article-title>Heterothallism in <italic>Cordyceps takaomontana</italic></article-title>. <source>FEMS Microbiol. Lett.</source><volume>250</volume>: <fpage>145</fpage>–<lpage>150</lpage><pub-id pub-id-type="pmid">16055279</pub-id></mixed-citation></ref><ref id="bib73"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yun</surname><given-names>S. H.</given-names></name><name><surname>Berbee</surname><given-names>M. L.</given-names></name><name><surname>Yoder</surname><given-names>O. C.</given-names></name><name><surname>Turgeon</surname><given-names>B. G.</given-names></name></person-group>, <year>1999</year> <article-title>Evolution of the fungal self-fertile reproductive life style from self-sterile ancestors</article-title>. <source>Proc. Natl. Acad. Sci. USA</source><volume>96</volume>: <fpage>5592</fpage>–<lpage>5597</lpage><pub-id pub-id-type="pmid">10318929</pub-id></mixed-citation></ref><ref id="bib74"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zaffarano</surname><given-names>P. L.</given-names></name><name><surname>Duò</surname><given-names>A.</given-names></name><name><surname>Grünig</surname><given-names>C. R.</given-names></name></person-group>, <year>2010</year> <article-title>Characterization of the mating-type (MAT) locus in the <italic>Phialocephala fortinii</italic> s. l. – <italic>Acephala applanata</italic> species complex</article-title>. <source>Fungal Genet. Biol.</source><volume>47</volume>: <fpage>761</fpage>–<lpage>772</lpage><pub-id pub-id-type="pmid">20541616</pub-id></mixed-citation></ref><ref id="bib75"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zipfel</surname><given-names>R. D.</given-names></name><name><surname>de Beer</surname><given-names>Z. W.</given-names></name><name><surname>Jacobs</surname><given-names>K.</given-names></name><name><surname>Wingfield</surname><given-names>B. D.</given-names></name><name><surname>Wingfield</surname><given-names>M. J.</given-names></name></person-group>, <year>2006</year> <article-title>Multi-gene phylogenis define <italic>Ceratocystiopsis</italic> and <italic>Grosmannia</italic> distinct from <italic>Ophiostoma</italic></article-title>. <source>Stud. Mycol.</source><volume>55</volume>: <fpage>75</fpage>–<lpage>97</lpage><pub-id pub-id-type="pmid">18490973</pub-id></mixed-citation></ref></ref-list></back></pmc></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Bois/explor/CheneBelgiqueV2/Data/Pmc/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000179 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Corpus/biblio.hfd -nk 000179 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Bois
|area= CheneBelgiqueV2
|flux= Pmc
|étape= Corpus
|type= RBID
|clé=
|texte=
}}
| This area was generated with Dilib version V0.6.27. |  |