Links to Exploration step
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block</title><author><name sortKey="Breen, James" sort="Breen, James" uniqKey="Breen J" first="James" last="Breen">James Breen</name><affiliation><nlm:aff id="I1">Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia</nlm:aff></affiliation><affiliation><nlm:aff id="I2">Molecular Plant Breeding Co-operative Research Centre (MPBCRC) Murdoch University, South Street, Perth 6150, Australia</nlm:aff></affiliation></author><author><name sortKey="Wicker, Thomas" sort="Wicker, Thomas" uniqKey="Wicker T" first="Thomas" last="Wicker">Thomas Wicker</name><affiliation><nlm:aff id="I3">Institute of Plant Biology, University Zurich, Zollikerstrasse 107, Zurich, CH-8008 Switzerland</nlm:aff></affiliation></author><author><name sortKey="Kong, Xiuying" sort="Kong, Xiuying" uniqKey="Kong X" first="Xiuying" last="Kong">Xiuying Kong</name><affiliation><nlm:aff id="I4">Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China</nlm:aff></affiliation></author><author><name sortKey="Zhang, Juncheng" sort="Zhang, Juncheng" uniqKey="Zhang J" first="Juncheng" last="Zhang">Juncheng Zhang</name><affiliation><nlm:aff id="I4">Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China</nlm:aff></affiliation></author><author><name sortKey="Ma, Wujun" sort="Ma, Wujun" uniqKey="Ma W" first="Wujun" last="Ma">Wujun Ma</name><affiliation><nlm:aff id="I1">Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia</nlm:aff></affiliation><affiliation><nlm:aff id="I5">State Agricultural Biotechnology Centre (SABC), Murdoch University, South Street, Perth 6150, Australia</nlm:aff></affiliation><affiliation><nlm:aff id="I6">Department of Agriculture and Food, Western Australia (DAFWA), 3 Baron Hay Court, Perth, 6151 Australia</nlm:aff></affiliation></author><author><name sortKey="Paux, Etienne" sort="Paux, Etienne" uniqKey="Paux E" first="Etienne" last="Paux">Etienne Paux</name><affiliation><nlm:aff id="I7">UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, INRA Site de Crouël, 63100 Clermont-ferrand, France</nlm:aff></affiliation></author><author><name sortKey="Feuillet, Catherine" sort="Feuillet, Catherine" uniqKey="Feuillet C" first="Catherine" last="Feuillet">Catherine Feuillet</name><affiliation><nlm:aff id="I7">UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, INRA Site de Crouël, 63100 Clermont-ferrand, France</nlm:aff></affiliation></author><author><name sortKey="Appels, Rudi" sort="Appels, Rudi" uniqKey="Appels R" first="Rudi" last="Appels">Rudi Appels</name><affiliation><nlm:aff id="I1">Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia</nlm:aff></affiliation></author><author><name sortKey="Bellgard, Matthew" sort="Bellgard, Matthew" uniqKey="Bellgard M" first="Matthew" last="Bellgard">Matthew Bellgard</name><affiliation><nlm:aff id="I1">Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">20507561</idno><idno type="pmc">3017796</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3017796</idno><idno type="RBID">PMC:3017796</idno><idno type="doi">10.1186/1471-2229-10-98</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">002300</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">002300</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block</title><author><name sortKey="Breen, James" sort="Breen, James" uniqKey="Breen J" first="James" last="Breen">James Breen</name><affiliation><nlm:aff id="I1">Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia</nlm:aff></affiliation><affiliation><nlm:aff id="I2">Molecular Plant Breeding Co-operative Research Centre (MPBCRC) Murdoch University, South Street, Perth 6150, Australia</nlm:aff></affiliation></author><author><name sortKey="Wicker, Thomas" sort="Wicker, Thomas" uniqKey="Wicker T" first="Thomas" last="Wicker">Thomas Wicker</name><affiliation><nlm:aff id="I3">Institute of Plant Biology, University Zurich, Zollikerstrasse 107, Zurich, CH-8008 Switzerland</nlm:aff></affiliation></author><author><name sortKey="Kong, Xiuying" sort="Kong, Xiuying" uniqKey="Kong X" first="Xiuying" last="Kong">Xiuying Kong</name><affiliation><nlm:aff id="I4">Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China</nlm:aff></affiliation></author><author><name sortKey="Zhang, Juncheng" sort="Zhang, Juncheng" uniqKey="Zhang J" first="Juncheng" last="Zhang">Juncheng Zhang</name><affiliation><nlm:aff id="I4">Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China</nlm:aff></affiliation></author><author><name sortKey="Ma, Wujun" sort="Ma, Wujun" uniqKey="Ma W" first="Wujun" last="Ma">Wujun Ma</name><affiliation><nlm:aff id="I1">Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia</nlm:aff></affiliation><affiliation><nlm:aff id="I5">State Agricultural Biotechnology Centre (SABC), Murdoch University, South Street, Perth 6150, Australia</nlm:aff></affiliation><affiliation><nlm:aff id="I6">Department of Agriculture and Food, Western Australia (DAFWA), 3 Baron Hay Court, Perth, 6151 Australia</nlm:aff></affiliation></author><author><name sortKey="Paux, Etienne" sort="Paux, Etienne" uniqKey="Paux E" first="Etienne" last="Paux">Etienne Paux</name><affiliation><nlm:aff id="I7">UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, INRA Site de Crouël, 63100 Clermont-ferrand, France</nlm:aff></affiliation></author><author><name sortKey="Feuillet, Catherine" sort="Feuillet, Catherine" uniqKey="Feuillet C" first="Catherine" last="Feuillet">Catherine Feuillet</name><affiliation><nlm:aff id="I7">UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, INRA Site de Crouël, 63100 Clermont-ferrand, France</nlm:aff></affiliation></author><author><name sortKey="Appels, Rudi" sort="Appels, Rudi" uniqKey="Appels R" first="Rudi" last="Appels">Rudi Appels</name><affiliation><nlm:aff id="I1">Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia</nlm:aff></affiliation></author><author><name sortKey="Bellgard, Matthew" sort="Bellgard, Matthew" uniqKey="Bellgard M" first="Matthew" last="Bellgard">Matthew Bellgard</name><affiliation><nlm:aff id="I1">Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia</nlm:aff></affiliation></author></analytic><series><title level="j">BMC Plant Biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The complexity of the wheat genome has resulted from waves of retrotransposable element insertions. Gene deletions and disruptions generated by the fast replacement of repetitive elements in wheat have resulted in disruption of colinearity at a micro (sub-megabase) level among the cereals. In view of genomic changes that are possible within a given time span, conservation of genes between species tends to imply an important functional or regional constraint that does not permit a change in genomic structure. The <italic>ctg1034 </italic>contig completed in this paper was initially studied because it was assigned to the <italic>Sr2 </italic>resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features.</p></sec><sec><title>Results</title><p>BAC shotgun sequencing of the hexaploid wheat (<italic>Triticum aestivum </italic>cv. Chinese Spring) genome has been used to assemble a group of 15 wheat BACs from the chromosome 3B physical map FPC contig <italic>ctg1034 </italic>into a 783,553 bp genomic sequence. This <italic>ctg1034 </italic>sequence was annotated for biological features such as genes and transposable elements. A three-gene island was identified among >80% repetitive DNA sequence. Using bioinformatics analysis there were no observable similarity in their gene functions. The <italic>ctg1034 </italic>gene island also displayed complete conservation of gene order and orientation with syntenic gene islands found in publicly available genome sequences of <italic>Brachypodium distachyon</italic>, <italic>Oryza sativa</italic>, <italic>Sorghum bicolor </italic>and <italic>Zea mays</italic>, even though the intergenic space and introns were divergent.</p></sec><sec><title>Conclusion</title><p>We propose that <italic>ctg1034 </italic>is located within the heterochromatic C-band region of deletion bin 3BL7 based on the identification of heterochromatic tandem repeats and presence of significant matches to chromodomain-containing <italic>gypsy </italic>LTR retrotransposable elements. We also speculate that this location, among other highly repetitive sequences, may account for the relative stability in gene order and orientation within the gene island.</p><p>Sequence data from this article have been deposited with the GenBank Data Libraries under accession no. GQ422824</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Gupta, Pk" uniqKey="Gupta P">PK Gupta</name></author><author><name sortKey="Mir, Rr" uniqKey="Mir R">RR Mir</name></author><author><name sortKey="Mohan, A" uniqKey="Mohan A">A Mohan</name></author><author><name sortKey="Kumar, J" uniqKey="Kumar J">J Kumar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gill, Bs" uniqKey="Gill B">BS Gill</name></author><author><name sortKey="Appels, R" uniqKey="Appels R">R Appels</name></author><author><name sortKey="Botha Oberholster, Am" uniqKey="Botha Oberholster A">AM Botha-Oberholster</name></author><author><name sortKey="Buell, Cr" uniqKey="Buell C">CR Buell</name></author><author><name sortKey="Bennetzen, Jl" uniqKey="Bennetzen J">JL Bennetzen</name></author><author><name sortKey="Chalhoub, B" uniqKey="Chalhoub B">B Chalhoub</name></author><author><name sortKey="Chumley, F" uniqKey="Chumley F">F Chumley</name></author><author><name sortKey="Dvorak, J" uniqKey="Dvorak J">J Dvorak</name></author><author><name sortKey="Iwanaga, M" uniqKey="Iwanaga M">M Iwanaga</name></author><author><name sortKey="Keller, B" uniqKey="Keller B">B Keller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wicker, T" uniqKey="Wicker T">T Wicker</name></author><author><name sortKey="Zimmermann, W" uniqKey="Zimmermann W">W Zimmermann</name></author><author><name sortKey="Perovic, D" uniqKey="Perovic D">D Perovic</name></author><author><name sortKey="Paterson, Ah" uniqKey="Paterson A">AH Paterson</name></author><author><name sortKey="Ganal, M" uniqKey="Ganal M">M Ganal</name></author><author><name sortKey="Graner, A" uniqKey="Graner A">A Graner</name></author><author><name sortKey="Stein, N" uniqKey="Stein N">N Stein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Paux, E" uniqKey="Paux E">E Paux</name></author><author><name sortKey="Sourdille, P" uniqKey="Sourdille P">P Sourdille</name></author><author><name sortKey="Salse, J" uniqKey="Salse J">J Salse</name></author><author><name sortKey="Saintenac, C" uniqKey="Saintenac C">C Saintenac</name></author><author><name sortKey="Choulet, F" uniqKey="Choulet F">F Choulet</name></author><author><name sortKey="Leroy, P" uniqKey="Leroy P">P Leroy</name></author><author><name sortKey="Korol, A" uniqKey="Korol A">A Korol</name></author><author><name sortKey="Michalak, M" uniqKey="Michalak M">M Michalak</name></author><author><name sortKey="Kianian, S" uniqKey="Kianian S">S Kianian</name></author><author><name sortKey="Spielmeyer, W" uniqKey="Spielmeyer W">W Spielmeyer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Charles, M" uniqKey="Charles M">M Charles</name></author><author><name sortKey="Belcram, H" uniqKey="Belcram H">H Belcram</name></author><author><name sortKey="Just, J" uniqKey="Just J">J Just</name></author><author><name sortKey="Huneau, C" uniqKey="Huneau C">C Huneau</name></author><author><name sortKey="Viollet, A" uniqKey="Viollet A">A Viollet</name></author><author><name sortKey="Couloux, A" uniqKey="Couloux A">A Couloux</name></author><author><name sortKey="Segurens, B" uniqKey="Segurens B">B Segurens</name></author><author><name sortKey="Carter, M" uniqKey="Carter M">M Carter</name></author><author><name sortKey="Huteau, V" uniqKey="Huteau V">V Huteau</name></author><author><name sortKey="Coriton, O" uniqKey="Coriton O">O Coriton</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dubcovsky, J" uniqKey="Dubcovsky J">J Dubcovsky</name></author><author><name sortKey="Ramakrishna, W" uniqKey="Ramakrishna W">W Ramakrishna</name></author><author><name sortKey="Sanmiguel, Pj" uniqKey="Sanmiguel P">PJ SanMiguel</name></author><author><name sortKey="Busso, Cs" uniqKey="Busso C">CS Busso</name></author><author><name sortKey="Yan, L" uniqKey="Yan L">L Yan</name></author><author><name sortKey="Shiloff, Ba" uniqKey="Shiloff B">BA Shiloff</name></author><author><name sortKey="Bennetzen, Jl" uniqKey="Bennetzen J">JL Bennetzen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Devos, Km" uniqKey="Devos K">KM Devos</name></author><author><name sortKey="Ma, J" uniqKey="Ma J">J Ma</name></author><author><name sortKey="Pontaroli, Ac" uniqKey="Pontaroli A">AC Pontaroli</name></author><author><name sortKey="Pratt, Lh" uniqKey="Pratt L">LH Pratt</name></author><author><name sortKey="Bennetzen, Jl" uniqKey="Bennetzen J">JL Bennetzen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dubcovsky, J" uniqKey="Dubcovsky J">J Dubcovsky</name></author><author><name sortKey="Dvorak, J" uniqKey="Dvorak J">J Dvorak</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Appels, R" uniqKey="Appels R">R Appels</name></author><author><name sortKey="Francki, M" uniqKey="Francki M">M Francki</name></author><author><name sortKey="Chibbar, R" uniqKey="Chibbar R">R Chibbar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yan, L" uniqKey="Yan L">L Yan</name></author><author><name sortKey="Loukoianov, A" uniqKey="Loukoianov A">A Loukoianov</name></author><author><name sortKey="Tranquilli, G" uniqKey="Tranquilli G">G Tranquilli</name></author><author><name sortKey="Helguera, M" uniqKey="Helguera M">M Helguera</name></author><author><name sortKey="Fahima, T" uniqKey="Fahima T">T Fahima</name></author><author><name sortKey="Dubcovsky, J" uniqKey="Dubcovsky J">J Dubcovsky</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sorrells, Me" uniqKey="Sorrells M">ME Sorrells</name></author><author><name sortKey="La Rota, M" uniqKey="La Rota M">M La Rota</name></author><author><name sortKey="Bermudez Kandianis, Ce" uniqKey="Bermudez Kandianis C">CE Bermudez-Kandianis</name></author><author><name sortKey="Greene, Ra" uniqKey="Greene R">RA Greene</name></author><author><name sortKey="Kantety, R" uniqKey="Kantety R">R Kantety</name></author><author><name sortKey="Munkvold, Jd" uniqKey="Munkvold J">JD Munkvold</name></author><author><name sortKey="Miftahudin" uniqKey="Miftahudin">Miftahudin</name></author><author><name sortKey="Mahmoud, A" uniqKey="Mahmoud A">A Mahmoud</name></author><author><name sortKey="Ma, X" uniqKey="Ma X">X Ma</name></author><author><name sortKey="Gustafson, Pj" uniqKey="Gustafson P">PJ Gustafson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Francki, M" uniqKey="Francki M">M Francki</name></author><author><name sortKey="Carter, M" uniqKey="Carter M">M Carter</name></author><author><name sortKey="Ryan, K" uniqKey="Ryan K">K Ryan</name></author><author><name sortKey="Hunter, A" uniqKey="Hunter A">A Hunter</name></author><author><name sortKey="Bellgard, M" uniqKey="Bellgard M">M Bellgard</name></author><author><name sortKey="Appels, R" uniqKey="Appels R">R Appels</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Todd, Ae" uniqKey="Todd A">AE Todd</name></author><author><name sortKey="Orengo, Ca" uniqKey="Orengo C">CA Orengo</name></author><author><name sortKey="Thornton, Jm" uniqKey="Thornton J">JM Thornton</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Paterson, Ah" uniqKey="Paterson A">AH Paterson</name></author><author><name sortKey="Bowers, Je" uniqKey="Bowers J">JE Bowers</name></author><author><name sortKey="Bruggmann, R" uniqKey="Bruggmann R">R Bruggmann</name></author><author><name sortKey="Dubchak, I" uniqKey="Dubchak I">I Dubchak</name></author><author><name sortKey="Grimwood, J" uniqKey="Grimwood J">J Grimwood</name></author><author><name sortKey="Gundlach, H" uniqKey="Gundlach H">H Gundlach</name></author><author><name sortKey="Haberer, G" uniqKey="Haberer G">G Haberer</name></author><author><name sortKey="Hellsten, U" uniqKey="Hellsten U">U Hellsten</name></author><author><name sortKey="Mitros, T" uniqKey="Mitros T">T Mitros</name></author><author><name sortKey="Poliakov, A" uniqKey="Poliakov A">A Poliakov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chantret, N" uniqKey="Chantret N">N Chantret</name></author><author><name sortKey="Cenci, A" uniqKey="Cenci A">A Cenci</name></author><author><name sortKey="Sabot, F" uniqKey="Sabot F">F Sabot</name></author><author><name sortKey="Anderson, Od" uniqKey="Anderson O">OD Anderson</name></author><author><name sortKey="Dubcovsky, J" uniqKey="Dubcovsky J">J Dubcovsky</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Faris, Jd" uniqKey="Faris J">JD Faris</name></author><author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name></author><author><name sortKey="Fellers, Jp" uniqKey="Fellers J">JP Fellers</name></author><author><name sortKey="Gill, Bs" uniqKey="Gill B">BS Gill</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sanmiguel, P" uniqKey="Sanmiguel P">P SanMiguel</name></author><author><name sortKey="Tikhonov, A" uniqKey="Tikhonov A">A Tikhonov</name></author><author><name sortKey="Jin, Yk" uniqKey="Jin Y">YK Jin</name></author><author><name sortKey="Motchoulskaia, N" uniqKey="Motchoulskaia N">N Motchoulskaia</name></author><author><name sortKey="Zakharov, D" uniqKey="Zakharov D">D Zakharov</name></author><author><name sortKey="Melake Berhan, A" uniqKey="Melake Berhan A">A Melake-Berhan</name></author><author><name sortKey="Springer, Ps" uniqKey="Springer P">PS Springer</name></author><author><name sortKey="Edwards, Kj" uniqKey="Edwards K">KJ Edwards</name></author><author><name sortKey="Lee, M" uniqKey="Lee M">M Lee</name></author><author><name sortKey="Avramova, Z" uniqKey="Avramova Z">Z Avramova</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Feuillet, C" uniqKey="Feuillet C">C Feuillet</name></author><author><name sortKey="Keller, B" uniqKey="Keller B">B Keller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tikhonov, Ap" uniqKey="Tikhonov A">AP Tikhonov</name></author><author><name sortKey="Sanmiguel, Pj" uniqKey="Sanmiguel P">PJ SanMiguel</name></author><author><name sortKey="Nakajima, Y" uniqKey="Nakajima Y">Y Nakajima</name></author><author><name sortKey="Gorenstein, Nm" uniqKey="Gorenstein N">NM Gorenstein</name></author><author><name sortKey="Bennetzen, Jl" uniqKey="Bennetzen J">JL Bennetzen</name></author><author><name sortKey="Avramova, Z" uniqKey="Avramova Z">Z Avramova</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wicker, T" uniqKey="Wicker T">T Wicker</name></author><author><name sortKey="Stein, N" uniqKey="Stein N">N Stein</name></author><author><name sortKey="Albar, L" uniqKey="Albar L">L Albar</name></author><author><name sortKey="Feuillet, C" uniqKey="Feuillet C">C Feuillet</name></author><author><name sortKey="Schlagenhauf, E" uniqKey="Schlagenhauf E">E Schlagenhauf</name></author><author><name sortKey="Keller, B" uniqKey="Keller B">B Keller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Caldwell, Ks" uniqKey="Caldwell K">KS Caldwell</name></author><author><name sortKey="Langridge, P" uniqKey="Langridge P">P Langridge</name></author><author><name sortKey="Powell, W" uniqKey="Powell W">W Powell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ewing, B" uniqKey="Ewing B">B Ewing</name></author><author><name sortKey="Green, P" uniqKey="Green P">P Green</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Paux, E" uniqKey="Paux E">E Paux</name></author><author><name sortKey="Roger, D" uniqKey="Roger D">D Roger</name></author><author><name sortKey="Badaeva, E" uniqKey="Badaeva E">E Badaeva</name></author><author><name sortKey="Gay, G" uniqKey="Gay G">G Gay</name></author><author><name sortKey="Bernard, M" uniqKey="Bernard M">M Bernard</name></author><author><name sortKey="Sourdille, P" uniqKey="Sourdille P">P Sourdille</name></author><author><name sortKey="Feuillet, C" uniqKey="Feuillet C">C Feuillet</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bartos, J" uniqKey="Bartos J">J Bartos</name></author><author><name sortKey="Paux, E" uniqKey="Paux E">E Paux</name></author><author><name sortKey="Kofler, R" uniqKey="Kofler R">R Kofler</name></author><author><name sortKey="Havrankova, M" uniqKey="Havrankova M">M Havrankova</name></author><author><name sortKey="Kopecky, D" uniqKey="Kopecky D">D Kopecky</name></author><author><name sortKey="Suchankova, P" uniqKey="Suchankova P">P Suchankova</name></author><author><name sortKey="Safar, J" uniqKey="Safar J">J Safar</name></author><author><name sortKey="Simkova, H" uniqKey="Simkova H">H Simkova</name></author><author><name sortKey="Town, Cd" uniqKey="Town C">CD Town</name></author><author><name sortKey="Lelley, T" uniqKey="Lelley T">T Lelley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lehmensiek, A" uniqKey="Lehmensiek A">A Lehmensiek</name></author><author><name sortKey="Eckermann, Pj" uniqKey="Eckermann P">PJ Eckermann</name></author><author><name sortKey="Verbyla, Ap" uniqKey="Verbyla A">AP Verbyla</name></author><author><name sortKey="Appels, R" uniqKey="Appels R">R Appels</name></author><author><name sortKey="Sutherland, Mw" uniqKey="Sutherland M">MW Sutherland</name></author><author><name sortKey="Daggard, Ge" uniqKey="Daggard G">GE Daggard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Gish, W" uniqKey="Gish W">W Gish</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author><author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name></author><author><name sortKey="Lipman, Dj" uniqKey="Lipman D">DJ Lipman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sonnhammer, El" uniqKey="Sonnhammer E">EL Sonnhammer</name></author><author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Novikova, O" uniqKey="Novikova O">O Novikova</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Eddy, Sr" uniqKey="Eddy S">SR Eddy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Novikova, O" uniqKey="Novikova O">O Novikova</name></author><author><name sortKey="Mayorov, V" uniqKey="Mayorov V">V Mayorov</name></author><author><name sortKey="Smyshlyaev, G" uniqKey="Smyshlyaev G">G Smyshlyaev</name></author><author><name sortKey="Fursov, M" uniqKey="Fursov M">M Fursov</name></author><author><name sortKey="Adkison, L" uniqKey="Adkison L">L Adkison</name></author><author><name sortKey="Pisarenko, O" uniqKey="Pisarenko O">O Pisarenko</name></author><author><name sortKey="Blinov, A" uniqKey="Blinov A">A Blinov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Paro, R" uniqKey="Paro R">R Paro</name></author><author><name sortKey="Hogness, Ds" uniqKey="Hogness D">DS Hogness</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Elgin, Sc" uniqKey="Elgin S">SC Elgin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Llorens, C" uniqKey="Llorens C">C Lloréns</name></author><author><name sortKey="Futami, R" uniqKey="Futami R">R Futami</name></author><author><name sortKey="Bezemer, D" uniqKey="Bezemer D">D Bezemer</name></author><author><name sortKey="Moya, A" uniqKey="Moya A">A Moya</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nagaki, K" uniqKey="Nagaki K">K Nagaki</name></author><author><name sortKey="Tsujimoto, H" uniqKey="Tsujimoto H">H Tsujimoto</name></author><author><name sortKey="Isono, K" uniqKey="Isono K">K Isono</name></author><author><name sortKey="Sasakuma, T" uniqKey="Sasakuma T">T Sasakuma</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, Q" uniqKey="Zhang Q">Q Zhang</name></author><author><name sortKey="Arbuckle, J" uniqKey="Arbuckle J">J Arbuckle</name></author><author><name sortKey="Wessler, Sr" uniqKey="Wessler S">SR Wessler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Majoros, Wh" uniqKey="Majoros W">WH Majoros</name></author><author><name sortKey="Pertea, M" uniqKey="Pertea M">M Pertea</name></author><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ouyang, S" uniqKey="Ouyang S">S Ouyang</name></author><author><name sortKey="Zhu, W" uniqKey="Zhu W">W Zhu</name></author><author><name sortKey="Hamilton, J" uniqKey="Hamilton J">J Hamilton</name></author><author><name sortKey="Lin, H" uniqKey="Lin H">H Lin</name></author><author><name sortKey="Campbell, M" uniqKey="Campbell M">M Campbell</name></author><author><name sortKey="Childs, K" uniqKey="Childs K">K Childs</name></author><author><name sortKey="Thibaud Nissen, F" uniqKey="Thibaud Nissen F">F Thibaud-Nissen</name></author><author><name sortKey="Malek, Rl" uniqKey="Malek R">RL Malek</name></author><author><name sortKey="Lee, Y" uniqKey="Lee Y">Y Lee</name></author><author><name sortKey="Zheng, L" uniqKey="Zheng L">L Zheng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kikuchi, S" uniqKey="Kikuchi S">S Kikuchi</name></author><author><name sortKey="Satoh, K" uniqKey="Satoh K">K Satoh</name></author><author><name sortKey="Nagata, T" uniqKey="Nagata T">T Nagata</name></author><author><name sortKey="Kawagashira, N" uniqKey="Kawagashira N">N Kawagashira</name></author><author><name sortKey="Doi, K" uniqKey="Doi K">K Doi</name></author><author><name sortKey="Kishimoto, N" uniqKey="Kishimoto N">N Kishimoto</name></author><author><name sortKey="Yazaki, J" uniqKey="Yazaki J">J Yazaki</name></author><author><name sortKey="Ishikawa, M" uniqKey="Ishikawa M">M Ishikawa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Silverstein, Ka" uniqKey="Silverstein K">KA Silverstein</name></author><author><name sortKey="Moskal, Wa" uniqKey="Moskal W">WA Moskal</name></author><author><name sortKey="Wu, Hc" uniqKey="Wu H">HC Wu</name></author><author><name sortKey="Underwood, Ba" uniqKey="Underwood B">BA Underwood</name></author><author><name sortKey="Graham, Ma" uniqKey="Graham M">MA Graham</name></author><author><name sortKey="Town, Cd" uniqKey="Town C">CD Town</name></author><author><name sortKey="Vandenbosch, Ka" uniqKey="Vandenbosch K">KA VandenBosch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Graham, Ma" uniqKey="Graham M">MA Graham</name></author><author><name sortKey="Silverstein, Ka" uniqKey="Silverstein K">KA Silverstein</name></author><author><name sortKey="Cannon, Sb" uniqKey="Cannon S">SB Cannon</name></author><author><name sortKey="Vandenbosch, Ka" uniqKey="Vandenbosch K">KA VandenBosch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ouyang, S" uniqKey="Ouyang S">S Ouyang</name></author><author><name sortKey="Buell, Cr" uniqKey="Buell C">CR Buell</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Jaillon, O" uniqKey="Jaillon O">O Jaillon</name></author><author><name sortKey="Aury, Jm" uniqKey="Aury J">JM Aury</name></author><author><name sortKey="Noel, B" uniqKey="Noel B">B Noel</name></author><author><name sortKey="Policriti, A" uniqKey="Policriti A">A Policriti</name></author><author><name sortKey="Clepet, C" uniqKey="Clepet C">C Clepet</name></author><author><name sortKey="Casagrande, A" uniqKey="Casagrande A">A Casagrande</name></author><author><name sortKey="Choisne, N" uniqKey="Choisne N">N Choisne</name></author><author><name sortKey="Aubourg, S" uniqKey="Aubourg S">S Aubourg</name></author><author><name sortKey="Vitulo, N" uniqKey="Vitulo N">N Vitulo</name></author><author><name sortKey="Jubin, C" uniqKey="Jubin C">C Jubin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tatusova, Ta" uniqKey="Tatusova T">TA Tatusova</name></author><author><name sortKey="Madden, Tl" uniqKey="Madden T">TL Madden</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chantret, N" uniqKey="Chantret N">N Chantret</name></author><author><name sortKey="Salse, J" uniqKey="Salse J">J Salse</name></author><author><name sortKey="Sabot, F" uniqKey="Sabot F">F Sabot</name></author><author><name sortKey="Bellec, A" uniqKey="Bellec A">A Bellec</name></author><author><name sortKey="Laubin, B" uniqKey="Laubin B">B Laubin</name></author><author><name sortKey="Dubois, I" uniqKey="Dubois I">I Dubois</name></author><author><name sortKey="Dossat, C" uniqKey="Dossat C">C Dossat</name></author><author><name sortKey="Sourdille, P" uniqKey="Sourdille P">P Sourdille</name></author><author><name sortKey="Joudrier, P" uniqKey="Joudrier P">P Joudrier</name></author><author><name sortKey="Gautier, Mf" uniqKey="Gautier M">MF Gautier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brooks, Sa" uniqKey="Brooks S">SA Brooks</name></author><author><name sortKey="Huang, L" uniqKey="Huang L">L Huang</name></author><author><name sortKey="Herbel, Mn" uniqKey="Herbel M">MN Herbel</name></author><author><name sortKey="Gill, Bs" uniqKey="Gill B">BS Gill</name></author><author><name sortKey="Brown Guedira, G" uniqKey="Brown Guedira G">G Brown-Guedira</name></author><author><name sortKey="Fellers, Jp" uniqKey="Fellers J">JP Fellers</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bennetzen, Jl" uniqKey="Bennetzen J">JL Bennetzen</name></author><author><name sortKey="Ramakrishna, W" uniqKey="Ramakrishna W">W Ramakrishna</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guyot, R" uniqKey="Guyot R">R Guyot</name></author><author><name sortKey="Yahiaoui, N" uniqKey="Yahiaoui N">N Yahiaoui</name></author><author><name sortKey="Feuillet, C" uniqKey="Feuillet C">C Feuillet</name></author><author><name sortKey="Keller, B" uniqKey="Keller B">B Keller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mefford, H" uniqKey="Mefford H">H Mefford</name></author><author><name sortKey="Sharp, A" uniqKey="Sharp A">A Sharp</name></author><author><name sortKey="Baker, C" uniqKey="Baker C">C Baker</name></author><author><name sortKey="Itsara, A" uniqKey="Itsara A">A Itsara</name></author><author><name sortKey="Jiang, Z" uniqKey="Jiang Z">Z Jiang</name></author><author><name sortKey="Buysse, K" uniqKey="Buysse K">K Buysse</name></author><author><name sortKey="Huang, S" uniqKey="Huang S">S Huang</name></author><author><name sortKey="Maloney, V" uniqKey="Maloney V">V Maloney</name></author><author><name sortKey="Crolla, J" uniqKey="Crolla J">J Crolla</name></author><author><name sortKey="Baralle, D" uniqKey="Baralle D">D Baralle</name></author><author><name sortKey="Collins, A" uniqKey="Collins A">A Collins</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kellogg, Ea" uniqKey="Kellogg E">EA Kellogg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lai, J" uniqKey="Lai J">J Lai</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y Li</name></author><author><name sortKey="Messing, J" uniqKey="Messing J">J Messing</name></author><author><name sortKey="Dooner, Hk" uniqKey="Dooner H">HK Dooner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lal, Sk" uniqKey="Lal S">SK Lal</name></author><author><name sortKey="Hannah, Lc" uniqKey="Hannah L">LC Hannah</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Buckler, Es" uniqKey="Buckler E">ES Buckler</name></author><author><name sortKey="Gaut, Bs" uniqKey="Gaut B">BS Gaut</name></author><author><name sortKey="Mcmullen, Md" uniqKey="Mcmullen M">MD McMullen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wicker, T" uniqKey="Wicker T">T Wicker</name></author><author><name sortKey="Guyot, R" uniqKey="Guyot R">R Guyot</name></author><author><name sortKey="Yahiaoui, N" uniqKey="Yahiaoui N">N Yahiaoui</name></author><author><name sortKey="Keller, B" uniqKey="Keller B">B Keller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sabot, F" uniqKey="Sabot F">F Sabot</name></author><author><name sortKey="Guyot, R" uniqKey="Guyot R">R Guyot</name></author><author><name sortKey="Wicker, T" uniqKey="Wicker T">T Wicker</name></author><author><name sortKey="Chantret, N" uniqKey="Chantret N">N Chantret</name></author><author><name sortKey="Laubin, B" uniqKey="Laubin B">B Laubin</name></author><author><name sortKey="Chalhoub, B" uniqKey="Chalhoub B">B Chalhoub</name></author><author><name sortKey="Leroy, P" uniqKey="Leroy P">P Leroy</name></author><author><name sortKey="Sourdille, P" uniqKey="Sourdille P">P Sourdille</name></author><author><name sortKey="Bernard, M" uniqKey="Bernard M">M Bernard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jiang, N" uniqKey="Jiang N">N Jiang</name></author><author><name sortKey="Bao, Z" uniqKey="Bao Z">Z Bao</name></author><author><name sortKey="Zhang, X" uniqKey="Zhang X">X Zhang</name></author><author><name sortKey="Eddy, Sr" uniqKey="Eddy S">SR Eddy</name></author><author><name sortKey="Wessler, Sr" uniqKey="Wessler S">SR Wessler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brooks, Sa" uniqKey="Brooks S">SA Brooks</name></author><author><name sortKey="Huang, L" uniqKey="Huang L">L Huang</name></author><author><name sortKey="Gill, Bs" uniqKey="Gill B">BS Gill</name></author><author><name sortKey="Fellers, Jp" uniqKey="Fellers J">JP Fellers</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qi, L" uniqKey="Qi L">L Qi</name></author><author><name sortKey="Echalier, B" uniqKey="Echalier B">B Echalier</name></author><author><name sortKey="Friebe, B" uniqKey="Friebe B">B Friebe</name></author><author><name sortKey="Gill, Bs" uniqKey="Gill B">BS Gill</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gill, Ks" uniqKey="Gill K">KS Gill</name></author><author><name sortKey="Gill, Bs" uniqKey="Gill B">BS Gill</name></author><author><name sortKey="Endo, Tr" uniqKey="Endo T">TR Endo</name></author><author><name sortKey="Taylor, T" uniqKey="Taylor T">T Taylor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Faris, Jd" uniqKey="Faris J">JD Faris</name></author><author><name sortKey="Haen, Km" uniqKey="Haen K">KM Haen</name></author><author><name sortKey="Gill, Bs" uniqKey="Gill B">BS Gill</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Komatsuda, T" uniqKey="Komatsuda T">T Komatsuda</name></author><author><name sortKey="Pourkheirandish, M" uniqKey="Pourkheirandish M">M Pourkheirandish</name></author><author><name sortKey="He, C" uniqKey="He C">C He</name></author><author><name sortKey="Azhaguvel, P" uniqKey="Azhaguvel P">P Azhaguvel</name></author><author><name sortKey="Kanamori, H" uniqKey="Kanamori H">H Kanamori</name></author><author><name sortKey="Perovic, D" uniqKey="Perovic D">D Perovic</name></author><author><name sortKey="Stein, N" uniqKey="Stein N">N Stein</name></author><author><name sortKey="Graner, A" uniqKey="Graner A">A Graner</name></author><author><name sortKey="Wicker, T" uniqKey="Wicker T">T Wicker</name></author><author><name sortKey="Tagiri, A" uniqKey="Tagiri A">A Tagiri</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dvorak, J" uniqKey="Dvorak J">J Dvorak</name></author><author><name sortKey="Akhunov, Ed" uniqKey="Akhunov E">ED Akhunov</name></author><author><name sortKey="Akhunov, Ar" uniqKey="Akhunov A">AR Akhunov</name></author><author><name sortKey="Deal, Kr" uniqKey="Deal K">KR Deal</name></author><author><name sortKey="Luo, Mc" uniqKey="Luo M">MC Luo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sanmiguel, Pj" uniqKey="Sanmiguel P">PJ SanMiguel</name></author><author><name sortKey="Ramakrishna, W" uniqKey="Ramakrishna W">W Ramakrishna</name></author><author><name sortKey="Bennetzen, Jl" uniqKey="Bennetzen J">JL Bennetzen</name></author><author><name sortKey="Busso, Cs" uniqKey="Busso C">CS Busso</name></author><author><name sortKey="Dubcovsky, J" uniqKey="Dubcovsky J">J Dubcovsky</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gao, X" uniqKey="Gao X">X Gao</name></author><author><name sortKey="Hou, Y" uniqKey="Hou Y">Y Hou</name></author><author><name sortKey="Ebina, H" uniqKey="Ebina H">H Ebina</name></author><author><name sortKey="Levin, Hl" uniqKey="Levin H">HL Levin</name></author><author><name sortKey="Voytas, Df" uniqKey="Voytas D">DF Voytas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kunzel, G" uniqKey="Kunzel G">G Künzel</name></author><author><name sortKey="Korzun, L" uniqKey="Korzun L">L Korzun</name></author><author><name sortKey="Meister, A" uniqKey="Meister A">A Meister</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chandler, Vl" uniqKey="Chandler V">VL Chandler</name></author><author><name sortKey="Alleman, M" uniqKey="Alleman M">M Alleman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Volpe, T" uniqKey="Volpe T">T Volpe</name></author><author><name sortKey="Schramke, V" uniqKey="Schramke V">V Schramke</name></author><author><name sortKey="Hamilton, Gl" uniqKey="Hamilton G">GL Hamilton</name></author><author><name sortKey="White, S" uniqKey="White S">S White</name></author><author><name sortKey="Teng, G" uniqKey="Teng G">G Teng</name></author><author><name sortKey="Martienssen, Ra" uniqKey="Martienssen R">RA Martienssen</name></author><author><name sortKey="Allshire, Rc" uniqKey="Allshire R">RC Allshire</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="May, Bp" uniqKey="May B">BP May</name></author><author><name sortKey="Lippman, Zb" uniqKey="Lippman Z">ZB Lippman</name></author><author><name sortKey="Fang, Y" uniqKey="Fang Y">Y Fang</name></author><author><name sortKey="Spector, Dl" uniqKey="Spector D">DL Spector</name></author><author><name sortKey="Martienssen, Ra" uniqKey="Martienssen R">RA Martienssen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vagin, Vv" uniqKey="Vagin V">VV Vagin</name></author><author><name sortKey="Sigova, A" uniqKey="Sigova A">A Sigova</name></author><author><name sortKey="Li, C" uniqKey="Li C">C Li</name></author><author><name sortKey="Seitz, H" uniqKey="Seitz H">H Seitz</name></author><author><name sortKey="Gvozdev, V" uniqKey="Gvozdev V">V Gvozdev</name></author><author><name sortKey="Zamore, Pd" uniqKey="Zamore P">PD Zamore</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, M" uniqKey="Kim M">M Kim</name></author><author><name sortKey="Vasiljeva, L" uniqKey="Vasiljeva L">L Vasiljeva</name></author><author><name sortKey="Rando, Oj" uniqKey="Rando O">OJ Rando</name></author><author><name sortKey="Zhelkovsky, A" uniqKey="Zhelkovsky A">A Zhelkovsky</name></author><author><name sortKey="Moore, C" uniqKey="Moore C">C Moore</name></author><author><name sortKey="Buratowski, S" uniqKey="Buratowski S">S Buratowski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sourdille, P" uniqKey="Sourdille P">P Sourdille</name></author><author><name sortKey="Singh, S" uniqKey="Singh S">S Singh</name></author><author><name sortKey="Cadalen, T" uniqKey="Cadalen T">T Cadalen</name></author><author><name sortKey="Brown Guedira, Gl" uniqKey="Brown Guedira G">GL Brown-Guedira</name></author><author><name sortKey="Gay, G" uniqKey="Gay G">G Gay</name></author><author><name sortKey="Qi, L" uniqKey="Qi L">L Qi</name></author><author><name sortKey="Gill, Bs" uniqKey="Gill B">BS Gill</name></author><author><name sortKey="Dufour, P" uniqKey="Dufour P">P Dufour</name></author><author><name sortKey="Murigneux, A" uniqKey="Murigneux A">A Murigneux</name></author><author><name sortKey="Bernard, M" uniqKey="Bernard M">M Bernard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Burge, C" uniqKey="Burge C">C Burge</name></author><author><name sortKey="Karlin, S" uniqKey="Karlin S">S Karlin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Finn, Rd" uniqKey="Finn R">RD Finn</name></author><author><name sortKey="Tate, J" uniqKey="Tate J">J Tate</name></author><author><name sortKey="Mistry, J" uniqKey="Mistry J">J Mistry</name></author><author><name sortKey="Coggill, Pc" uniqKey="Coggill P">PC Coggill</name></author><author><name sortKey="Sammut, Sj" uniqKey="Sammut S">SJ Sammut</name></author><author><name sortKey="Hotz, Hr" uniqKey="Hotz H">HR Hotz</name></author><author><name sortKey="Ceric, G" uniqKey="Ceric G">G Ceric</name></author><author><name sortKey="Forslund, K" uniqKey="Forslund K">K Forslund</name></author><author><name sortKey="Eddy, Sr" uniqKey="Eddy S">SR Eddy</name></author><author><name sortKey="Sonnhammer, El" uniqKey="Sonnhammer E">EL Sonnhammer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marchler Bauer, A" uniqKey="Marchler Bauer A">A Marchler-Bauer</name></author><author><name sortKey="Anderson, Jb" uniqKey="Anderson J">JB Anderson</name></author><author><name sortKey="Derbyshire, Mk" uniqKey="Derbyshire M">MK Derbyshire</name></author><author><name sortKey="Deweese Scott, C" uniqKey="Deweese Scott C">C DeWeese-Scott</name></author><author><name sortKey="Gonzales, Nr" uniqKey="Gonzales N">NR Gonzales</name></author><author><name sortKey="Gwadz, M" uniqKey="Gwadz M">M Gwadz</name></author><author><name sortKey="Hao, L" uniqKey="Hao L">L Hao</name></author><author><name sortKey="He, S" uniqKey="He S">S He</name></author><author><name sortKey="Hurwitz, Di" uniqKey="Hurwitz D">DI Hurwitz</name></author><author><name sortKey="Jackson, Jd" uniqKey="Jackson J">JD Jackson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Quevillon, E" uniqKey="Quevillon E">E Quevillon</name></author><author><name sortKey="Silventoinen, V" uniqKey="Silventoinen V">V Silventoinen</name></author><author><name sortKey="Pillai, S" uniqKey="Pillai S">S Pillai</name></author><author><name sortKey="Harte, N" uniqKey="Harte N">N Harte</name></author><author><name sortKey="Mulder, N" uniqKey="Mulder N">N Mulder</name></author><author><name sortKey="Apweiler, R" uniqKey="Apweiler R">R Apweiler</name></author><author><name sortKey="Lopez, R" uniqKey="Lopez R">R Lopez</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Apweiler, R" uniqKey="Apweiler R">R Apweiler</name></author><author><name sortKey="Attwood, Tk" uniqKey="Attwood T">TK Attwood</name></author><author><name sortKey="Bairoch, A" uniqKey="Bairoch A">A Bairoch</name></author><author><name sortKey="Bateman, A" uniqKey="Bateman A">A Bateman</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author><author><name sortKey="Biswas, M" uniqKey="Biswas M">M Biswas</name></author><author><name sortKey="Bucher, P" uniqKey="Bucher P">P Bucher</name></author><author><name sortKey="Cerutti, L" uniqKey="Cerutti L">L Cerutti</name></author><author><name sortKey="Corpet, F" uniqKey="Corpet F">F Corpet</name></author><author><name sortKey="Croning, Md" uniqKey="Croning M">MD Croning</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thompson, Jd" uniqKey="Thompson J">JD Thompson</name></author><author><name sortKey="Gibson, Tj" uniqKey="Gibson T">TJ Gibson</name></author><author><name sortKey="Higgins, Dg" uniqKey="Higgins D">DG Higgins</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schwartz, S" uniqKey="Schwartz S">S Schwartz</name></author><author><name sortKey="Elnitski, L" uniqKey="Elnitski L">L Elnitski</name></author><author><name sortKey="Li, M" uniqKey="Li M">M Li</name></author><author><name sortKey="Weirauch, M" uniqKey="Weirauch M">M Weirauch</name></author><author><name sortKey="Riemer, C" uniqKey="Riemer C">C Riemer</name></author><author><name sortKey="Smit, A" uniqKey="Smit A">A Smit</name></author><author><name sortKey="Program, Ncs" uniqKey="Program N">NCS Program</name></author><author><name sortKey="Green, Ed" uniqKey="Green E">ED Green</name></author><author><name sortKey="Hardison, Rc" uniqKey="Hardison R">RC Hardison</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nozaki, Y" uniqKey="Nozaki Y">Y Nozaki</name></author><author><name sortKey="Macgregor, A" uniqKey="Macgregor A">A Macgregor</name></author><author><name sortKey="Smith, C" uniqKey="Smith C">C Smith</name></author><author><name sortKey="Hunter, A" uniqKey="Hunter A">A Hunter</name></author><author><name sortKey="Bellgard, M" uniqKey="Bellgard M">M Bellgard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Darling, Ac" uniqKey="Darling A">AC Darling</name></author><author><name sortKey="Mau, B" uniqKey="Mau B">B Mau</name></author><author><name sortKey="Blattner, Fr" uniqKey="Blattner F">FR Blattner</name></author><author><name sortKey="Perna, Nt" uniqKey="Perna N">NT Perna</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carver, Tj" uniqKey="Carver T">TJ Carver</name></author><author><name sortKey="Rutherford, Km" uniqKey="Rutherford K">KM Rutherford</name></author><author><name sortKey="Berriman, M" uniqKey="Berriman M">M Berriman</name></author><author><name sortKey="Rajandream, Ma" uniqKey="Rajandream M">MA Rajandream</name></author><author><name sortKey="Barrell, Bg" uniqKey="Barrell B">BG Barrell</name></author><author><name sortKey="Parkhill, J" uniqKey="Parkhill J">J Parkhill</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">BMC Plant Biol</journal-id><journal-title-group><journal-title>BMC Plant Biology</journal-title></journal-title-group><issn pub-type="epub">1471-2229</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">20507561</article-id><article-id pub-id-type="pmc">3017796</article-id><article-id pub-id-type="publisher-id">1471-2229-10-98</article-id><article-id pub-id-type="doi">10.1186/1471-2229-10-98</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block</article-title></title-group><contrib-group><contrib contrib-type="author" id="A1"><name><surname>Breen</surname><given-names>James</given-names></name><xref ref-type="aff" rid="I1">1</xref><xref ref-type="aff" rid="I2">2</xref><email>jbreen@ccg.murdoch.edu.au</email></contrib><contrib contrib-type="author" id="A2"><name><surname>Wicker</surname><given-names>Thomas</given-names></name><xref ref-type="aff" rid="I3">3</xref><email>wicker@botinst.unizh.ch</email></contrib><contrib contrib-type="author" id="A3"><name><surname>Kong</surname><given-names>Xiuying</given-names></name><xref ref-type="aff" rid="I4">4</xref><email>xykong@mail.caas.net.cn</email></contrib><contrib contrib-type="author" id="A4"><name><surname>Zhang</surname><given-names>Juncheng</given-names></name><xref ref-type="aff" rid="I4">4</xref><email>jczhang2008@163.com</email></contrib><contrib contrib-type="author" id="A5"><name><surname>Ma</surname><given-names>Wujun</given-names></name><xref ref-type="aff" rid="I1">1</xref><xref ref-type="aff" rid="I5">5</xref><xref ref-type="aff" rid="I6">6</xref><email>W.Ma@murdoch.edu.au</email></contrib><contrib contrib-type="author" id="A6"><name><surname>Paux</surname><given-names>Etienne</given-names></name><xref ref-type="aff" rid="I7">7</xref><email>etienne.paux@clermont.inra.fr</email></contrib><contrib contrib-type="author" id="A7"><name><surname>Feuillet</surname><given-names>Catherine</given-names></name><xref ref-type="aff" rid="I7">7</xref><email>catherine.feuillet@clermont.inra.fr</email></contrib><contrib contrib-type="author" corresp="yes" id="A8"><name><surname>Appels</surname><given-names>Rudi</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>rappels@ccg.murdoch.edu.au</email></contrib><contrib contrib-type="author" id="A9"><name><surname>Bellgard</surname><given-names>Matthew</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>mbellgard@ccg.murdoch.edu.au</email></contrib></contrib-group><aff id="I1"><label>1</label>Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia</aff><aff id="I2"><label>2</label>Molecular Plant Breeding Co-operative Research Centre (MPBCRC) Murdoch University, South Street, Perth 6150, Australia</aff><aff id="I3"><label>3</label>Institute of Plant Biology, University Zurich, Zollikerstrasse 107, Zurich, CH-8008 Switzerland</aff><aff id="I4"><label>4</label>Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China</aff><aff id="I5"><label>5</label>State Agricultural Biotechnology Centre (SABC), Murdoch University, South Street, Perth 6150, Australia</aff><aff id="I6"><label>6</label>Department of Agriculture and Food, Western Australia (DAFWA), 3 Baron Hay Court, Perth, 6151 Australia</aff><aff id="I7"><label>7</label>UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, INRA Site de Crouël, 63100 Clermont-ferrand, France</aff><pub-date pub-type="collection"><year>2010</year></pub-date><pub-date pub-type="epub"><day>27</day><month>5</month><year>2010</year></pub-date><volume>10</volume><fpage>98</fpage><lpage>98</lpage><history><date date-type="received"><day>27</day><month>8</month><year>2009</year></date><date date-type="accepted"><day>27</day><month>5</month><year>2010</year></date></history><permissions><copyright-statement>Copyright ©2010 Breen et al; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2010</copyright-year><copyright-holder>Breen et al; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</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:href="http://www.biomedcentral.com/1471-2229/10/98"></self-uri><abstract><sec><title>Background</title><p>The complexity of the wheat genome has resulted from waves of retrotransposable element insertions. Gene deletions and disruptions generated by the fast replacement of repetitive elements in wheat have resulted in disruption of colinearity at a micro (sub-megabase) level among the cereals. In view of genomic changes that are possible within a given time span, conservation of genes between species tends to imply an important functional or regional constraint that does not permit a change in genomic structure. The <italic>ctg1034 </italic>contig completed in this paper was initially studied because it was assigned to the <italic>Sr2 </italic>resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features.</p></sec><sec><title>Results</title><p>BAC shotgun sequencing of the hexaploid wheat (<italic>Triticum aestivum </italic>cv. Chinese Spring) genome has been used to assemble a group of 15 wheat BACs from the chromosome 3B physical map FPC contig <italic>ctg1034 </italic>into a 783,553 bp genomic sequence. This <italic>ctg1034 </italic>sequence was annotated for biological features such as genes and transposable elements. A three-gene island was identified among >80% repetitive DNA sequence. Using bioinformatics analysis there were no observable similarity in their gene functions. The <italic>ctg1034 </italic>gene island also displayed complete conservation of gene order and orientation with syntenic gene islands found in publicly available genome sequences of <italic>Brachypodium distachyon</italic>, <italic>Oryza sativa</italic>, <italic>Sorghum bicolor </italic>and <italic>Zea mays</italic>, even though the intergenic space and introns were divergent.</p></sec><sec><title>Conclusion</title><p>We propose that <italic>ctg1034 </italic>is located within the heterochromatic C-band region of deletion bin 3BL7 based on the identification of heterochromatic tandem repeats and presence of significant matches to chromodomain-containing <italic>gypsy </italic>LTR retrotransposable elements. We also speculate that this location, among other highly repetitive sequences, may account for the relative stability in gene order and orientation within the gene island.</p><p>Sequence data from this article have been deposited with the GenBank Data Libraries under accession no. GQ422824</p></sec></abstract></article-meta></front><body><sec><title>Background</title><p>Wheat (<italic>Triticum aestivum</italic>) is one of the major food crops in the world, providing 20% of the total food calories and protein in human nutrition [<xref ref-type="bibr" rid="B1">1</xref>] but its large genome size (~16000 Mb) and complexity (~80% repetitive sequences) has hindered genome sequencing studies [<xref ref-type="bibr" rid="B2">2</xref>]. To date, the largest sequenced, assembled and annotated genomic sequence from BAC clones from Triticeae genomes is 439 kb [<xref ref-type="bibr" rid="B3">3</xref>]. The recent publication of the physical map of the largest wheat chromosome 3B [<xref ref-type="bibr" rid="B4">4</xref>], along with other mapping projects initiated within the international wheat genome sequencing consortium (IWGSC), has established a platform for more extensive sequencing studies.</p><p>The high complexity of the wheat genome produced by such factors as retrotransposable element insertion [<xref ref-type="bibr" rid="B5">5</xref>] and polyploidy, has complicated comparisons between the genomes of closely related species. Gene deletions and disruptions generated by the fast replacement of repetitive elements in wheat [<xref ref-type="bibr" rid="B6">6</xref>-<xref ref-type="bibr" rid="B8">8</xref>], have resulted in loss of colinearity at a micro (sub-megabase) level [<xref ref-type="bibr" rid="B9">9</xref>-<xref ref-type="bibr" rid="B12">12</xref>]. In view of genomic changes that are possible within a given time span, conservation of gene structure, order and orientation between species tends to imply an important functional or regional constraint that does not permit a change in genomic structure [<xref ref-type="bibr" rid="B13">13</xref>]. The <italic>ctg1034 </italic>sequence characterized in the present study is a good example of such high conservation of structure.</p><p>The availability of finished, whole genome sequences for rice (<italic>Oryza sativa</italic>) [<xref ref-type="bibr" rid="B14">14</xref>] and <italic>Sorghum bicolor </italic>[<xref ref-type="bibr" rid="B15">15</xref>], as well as extensive sequencing of the maize (<italic>Zea mays</italic>; <ext-link ext-link-type="uri" xlink:href="http://www.maizesequence.org">http://www.maizesequence.org</ext-link>) and Brachypodium (<italic>Brachypodium distachyon </italic><ext-link ext-link-type="uri" xlink:href="http://www.brachypodium.org">http://www.brachypodium.org</ext-link>) genomes, has provided a basis for a detailed analysis of colinearity. Due to a lack of whole genome sequence data for wheat, micro-colinearity has been confirmed on individual sequenced genetic loci of agronomically important genes [<xref ref-type="bibr" rid="B16">16</xref>,<xref ref-type="bibr" rid="B17">17</xref>] but little work has been carried out to identify any detailed relationships in regions of low gene density.</p><p>Gene islands exist in grass genomes [<xref ref-type="bibr" rid="B18">18</xref>-<xref ref-type="bibr" rid="B21">21</xref>] and gene-densities of over one gene every 20 kb have been reported [<xref ref-type="bibr" rid="B7">7</xref>,<xref ref-type="bibr" rid="B22">22</xref>]. On wheat chromosome 3B, Charles et al. [<xref ref-type="bibr" rid="B5">5</xref>] carried out random BAC sequencing to identify transposable element distribution and annotated the very few active genes within distal regions of the long-arm of the chromosome. Only one gene island (containing two active genes) was identified out of the 10 annotated BAC clones.</p><p>In this study we report on the sequencing of a group of 15 BACs located within FPC <italic>ctg1034 </italic>from the hexaploid wheat chromosome 3B physical map [<xref ref-type="bibr" rid="B4">4</xref>], and their assembly into a 783,553 bp genomic sequence. This large genomic sequence is among the first reported for the long arm of chromosome 3B and is also one of the largest and most complete genomic sequences described for wheat. The 783,553 bp genomic sequence was initially studied because it was assigned to the <italic>Sr2 </italic>resistance locus region, however detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features. Annotation of <italic>ctg1034 </italic>through bioinformatics analysis identified a conserved gene island containing three genes of different gene function. Comparative analysis with five other cereal genomes revealed the highly conserved nature of the gene island despite no apparent co-expression or other shared functional attributes being identified.</p></sec><sec><title>Results</title><sec><title><italic>Ctg1034 </italic>sequence assembly and chromosome 3B mapping</title><p>The sequencing of chromosome 3B-<italic>ctg1034 </italic>from <italic>Triticum aestivum </italic>cv. Chinese Spring was initially carried out using a BAC-by-BAC shotgun method at a 6× sequencing coverage. Twelve BACs (026-I13, 025-I18, 077-L15, 059-E04, 052-J13, 010-K23, 111-P10, 064-A05, 050-O19, 112-J14, 089-H14 and 015-L23) were originally selected from the chromosome 3B physical map generated by FPC mapping [<xref ref-type="bibr" rid="B4">4</xref>] (Figure <xref ref-type="fig" rid="F1">1</xref>). Gap closure was carried out by identifying sequence read pairs and designing primers to extend the genomic sequence. A second set of four BAC clones (029-L04, 044-J13, 159-L15 and 050-K20) was sequenced at 10× coverage in an attempt to close all remaining genomic sequence gaps (Figure <xref ref-type="fig" rid="F1">1</xref>). The sixteen wheat BACs were assembled using the Phred/Phrap sequence assembly package [<xref ref-type="bibr" rid="B23">23</xref>]. BAC contigs were ordered and assembled into a scaffold sequence by using target site duplications (TSDs) located at the ends of transposable elements (T. Wicker et al manuscript <italic>in preparation</italic>). TSDs associated with a particular transposable element allowed this element to be annotated even if nested insertions had occurred within it to complicate its internal structure.</p><fig id="F1" position="float"><label>Figure 1</label><caption><p><bold>Genome sequence annotation of <italic>ctg1034 </italic>showing the wheat BAC clones that were used in the assembly of the genomic sequence</bold>. The retrotransposable elements have been color coded as indicated in the insert.</p></caption><graphic xlink:href="1471-2229-10-98-1"></graphic></fig><p>The BAC contigs sequenced in this study were initially linked to BACs located in the region of the <italic>Sr2 </italic>locus (Mago et al. <italic>in preparation</italic>) of chromosome 3BS and the contig was of interest because of the identification of a defensin gene within the gene island. However, when no overlap could be found within assembled contigs, markers were tested to re-examine the chromosome location of the BACs. Two insertion site based polymorphism (ISBP) markers [<xref ref-type="bibr" rid="B7">7</xref>,<xref ref-type="bibr" rid="B24">24</xref>,<xref ref-type="bibr" rid="B25">25</xref>] were identified in the sequence and used to screen the Cranbrook × Halberd mapping population [<xref ref-type="bibr" rid="B26">26</xref>] to find the chromosomal location of <italic>ctg1034 </italic>on chromosome 3B. Figure <xref ref-type="fig" rid="F2">2(A)</xref> shows the genetic mapping analysis results on the Cranbrook × Halberd mapping population which confirmed earlier indications from studies using a French (INRA) mapping population that contig 1034 was co-located with molecular markers previously assigned to bin 3BL-7, on the long arm of 3B. Confirmation of the location in bin 3BL7 is provided in Figure <xref ref-type="fig" rid="F2">2B</xref> using the same ISBP markers used for the genetic mapping. The ISBP Sc3-119 marker primers (predicted PCR band size of 158 bp) showed multiple PCR bands with the band of the expected size missing from lanes 4 and 5. For ISBP Sc3-120, the PCR showed a single band of the expected size (190 bp) and this band was missing in lanes 4 and 5. Since lanes 3 and 4 are deletion lines 3BL10 and 3BL7 the analysis indicated that the locus containing the ISBP is located on 3BL7 [<xref ref-type="bibr" rid="B4">4</xref>].</p><fig id="F2" position="float"><label>Figure 2</label><caption><p><bold>Location of <italic>ctg1034</italic></bold>. A (left panel). Genetic mapping using two ISBP markers, Sc3-119 and Sc3-120 on the Cranbrook × Halberd population [<xref ref-type="bibr" rid="B26">26</xref>] demonstrated a co-location with markers assigned to bin3BL-7 on the long arm location on 3B [<xref ref-type="bibr" rid="B72">72</xref>]. The genetic map shows a small part of the map (complete map, Cran*Hal 3B Feb09, is available at <ext-link ext-link-type="uri" xlink:href="http://ccg.murdoch.edu.au/cmap/ccg-live/">http://ccg.murdoch.edu.au/cmap/ccg-live/</ext-link>). B (right panel). The bin 3BL-7 region of chromosome 3B is characterized by the SSRs Xgwm299, Xgwm2152, Xgwm547, Xgwm247, Xgwm340, Xgwm181, Xfwm4, Xcfa2170, Xbarc84, Xpsr170, XksuG62 [<xref ref-type="bibr" rid="B72">72</xref>] and the two ISBP markers (Sc3-119 and Sc3-120) could be assigned to this deletion bin. Lane 1-8 on the electrophoresis gel on the left-hand panel of the figure indicates the analysis of Sc3-119 and Sc3-120 with the deletion bins of chromosome 3B (lane 1: 3BS-8, lane 2: 3BS-9, lane 3: 3BS-1, lane 4: 3BL-10, lane 5: 3BL-7, lane 6: Halberd and lane 7: Cranbrook).</p></caption><graphic xlink:href="1471-2229-10-98-2"></graphic></fig></sec><sec><title>Transposable element annotation of <italic>ctg1034</italic></title><p>Transposable elements (TEs) were annotated in this study using BLASTN and BLASTX [<xref ref-type="bibr" rid="B27">27</xref>] sequence homology searches against the non-redundant nucleotide (e-value < 1e<sup>-30</sup>) and protein (e-value < 1e<sup>-10</sup>) sets of the Triticeae repetitive element (TREP) database. Alignments to TEs located within <italic>ctg1034 </italic>were confirmed using the DOTTER dot-matrix program [<xref ref-type="bibr" rid="B28">28</xref>] and were used to identify target site duplications (TSDs) at either end of the element. Table <xref ref-type="table" rid="T1">1</xref> lists the TE families that are distributed within <italic>ctg1034 </italic>and their sequence proportions compared to the rest of the assembled contig.</p><table-wrap id="T1" position="float"><label>Table 1</label><caption><p>Transposable element Annotation of Chromosome 3B <italic>ctg1034</italic></p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left">Class</th><th align="center">Order</th><th align="center">Family</th><th align="center">Code</th><th align="center">Elements</th><th align="center">Complete TSD</th><th align="center">Nested</th><th align="center">Length (bp)</th><th align="center">% TEs</th><th align="center">% Contig</th></tr></thead><tbody><tr><td align="left">Class I <break></break>(Retrotransposable elements)</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td></td><td align="center">LINE</td><td align="center">Unknown</td><td align="center">RIX</td><td align="center">1</td><td></td><td align="center">1</td><td align="center">2962</td><td align="center">0.46%</td><td align="center">0.38%</td></tr><tr><td></td><td align="center">LTR</td><td align="center">Copia</td><td align="center">RLC</td><td align="center">9</td><td align="center">9</td><td align="center">1</td><td align="center">93966</td><td align="center">14.66%</td><td align="center">11.99%</td></tr><tr><td></td><td></td><td align="center">Gypsy</td><td align="center">RLG</td><td align="center">55</td><td align="center">39</td><td align="center">19</td><td align="center">401485</td><td align="center">62.64%</td><td align="center">51.24%</td></tr><tr><td></td><td></td><td align="center">Unknown</td><td align="center">RLX</td><td align="center">6</td><td align="center">3</td><td align="center">2</td><td align="center">29915</td><td align="center">4.67%</td><td align="center">3.82%</td></tr><tr><td align="left">Total</td><td></td><td></td><td></td><td align="center"><bold>71</bold></td><td align="center"><bold>51</bold></td><td align="center"><bold>23</bold></td><td align="center"><bold>528328</bold></td><td align="center"><bold>82.42%</bold></td><td align="center"><bold>67.43%</bold></td></tr><tr><td align="left">Class II (DNA Transposons)</td><td align="center">TIR</td><td align="center">CACTA</td><td align="center">DTC</td><td align="center">9</td><td align="center">5</td><td align="center">5</td><td align="center">100864</td><td align="center">15.74%</td><td align="center">12.87%</td></tr><tr><td></td><td></td><td align="center">Harbinger</td><td align="center">DTH</td><td align="center">1</td><td></td><td></td><td align="center">1838</td><td align="center">0.29%</td><td align="center">0.23%</td></tr><tr><td></td><td></td><td align="center">Mutator</td><td align="center">DTM</td><td align="center">1</td><td></td><td></td><td align="center">802</td><td align="center">0.13%</td><td align="center">0.10%</td></tr><tr><td></td><td></td><td align="center">Tc1- mariner</td><td align="center">DTT</td><td align="right">1</td><td></td><td></td><td align="center">693</td><td align="center">0.11%</td><td align="center">0.09%</td></tr><tr><td></td><td align="center">Unknown</td><td></td><td align="center">DXX</td><td align="center">1</td><td></td><td></td><td align="center">730</td><td align="center">0.11%</td><td align="center">0.09%</td></tr><tr><td align="left">Total</td><td></td><td></td><td></td><td align="center"><bold>13</bold></td><td align="center"><bold>5</bold></td><td align="center"><bold>5</bold></td><td align="center"><bold>104927</bold></td><td align="center"><bold>16.37%</bold></td><td align="center"><bold>13.39%</bold></td></tr><tr><td align="left">Unknown</td><td></td><td></td><td align="center">XXX</td><td align="center">2</td><td></td><td></td><td align="center">7733</td><td align="center">1.21%</td><td align="center">0.99%</td></tr><tr><td align="left">Total Transposable elements</td><td></td><td></td><td></td><td align="center"><bold>86</bold></td><td align="center"><bold>56</bold></td><td align="center"><bold>28</bold></td><td align="center"><bold>640988</bold></td><td></td><td align="center"><bold>81.81%</bold></td></tr></tbody></table></table-wrap><p>Overall, TEs made up 81.8% of the entire <italic>ctg1034 </italic>chromosome 3B sequence. The repetitive element content was dominated by retrotransposable elements (class I TEs, 82.42% of all TEs and 67.43% of the entire contig), considered to transpose through the action of a RNA intermediate. This was compared to the DNA transposons (class II), which comprised only 16.37% of all TEs (13.39% of the total contig). The <italic>gypsy </italic>family of long terminal repeat (LTR) retrotransposable elements were by far the most abundant type of class I-TE, with 71 out of the 86 transposons found (51 of which were complete with intact TSDs) and occupying more than half the total sequence of <italic>ctg1034 </italic>(51.24%).</p><p>Two <italic>gypsy </italic>elements, <italic>Romani </italic>located at 698,865 - 709732 bp and <italic>Latidu </italic>located at 510,556 - 523623 bp in <italic>ctg1034</italic>, were also found to contain significant matches to chromodomains, which are located in the C-terminal region of the integrase (IN) protein domain of the <italic>gypsy </italic>internal polyprotein (<italic>gag-pol</italic>) domain [<xref ref-type="bibr" rid="B29">29</xref>]. A profile HMM [<xref ref-type="bibr" rid="B30">30</xref>] constructed using consensus sequences of <italic>reverse transcriptase </italic>(RT) and IN domains in [<xref ref-type="bibr" rid="B31">31</xref>] was used to identify potential chromodomain matches (e-values of 5.7e<sup>-307 </sup>and 1.5e<sup>-303 </sup>for <italic>Romani </italic>and <italic>Latidu </italic>respectively). Chromodomains were originally identified in the centromeric heterochromatin proteins of <italic>Drosophila </italic>[<xref ref-type="bibr" rid="B32">32</xref>,<xref ref-type="bibr" rid="B33">33</xref>] and have been argued to target heterochromatin by recognizing histone modifications [<xref ref-type="bibr" rid="B31">31</xref>]. The internal regions of both the <italic>Romani </italic>and <italic>Latidu </italic>LTR <italic>gypsy </italic>elements were also searched using BLASTX against the characterised internal domains of the <italic>gypsy </italic>mobile genetic element database (GyDB) [<xref ref-type="bibr" rid="B34">34</xref>]. Both elements contained significant matches (evalue of 1e<sup>-149</sup>) to the integrase domain of the <italic>O.sativa </italic>LTR <italic>gypsy </italic>element <italic>Retrosat-2</italic>.</p><p>The <italic>CACTA </italic>DNA transposons and <italic>copia </italic>LTR families were also well represented with 12.87% and 11.99% of the total <italic>ctg1034 </italic>sequence respectively. The <italic>CACTA </italic>DNA transposons had a high proportion of elements (5 out of the 9 elements found) that contained nested insertions. <italic>Gypsy </italic>LTR retrotransposons had a slightly lower proportion of nested elements (19 out of 55). The <italic>copia </italic>LTR elements were found to be the most intact with only one element containing a nested insertion and all identified to be complete with TSDs.</p><p>Tandem repeats considered to be located within heterochromatic regions in Triticeae genomes were also assayed to identify matches to <italic>ctg1034</italic>. Two matches were genome specific' <italic>Aegilops squarrosa </italic>repetitive DNA sequence (GenBank accession: D30736) [<xref ref-type="bibr" rid="B35">35</xref>] and the other being an <italic>Aegilops tauschii </italic>so-called centromeric-specific tandem repeat from clone 6C6-3 (Genbank accession: AY249982) [<xref ref-type="bibr" rid="B36">36</xref>]. The well-studied D30736 repeat [<xref ref-type="bibr" rid="B35">35</xref>] is from the <italic>Afa1 </italic>family of tandem repeats (based on the restriction enzyme site) and is made up of 240 bp units, only one of which was located in the <italic>ctg1034 </italic>sequence between 72,048 and 72,279 bp (89% nucleotide identity over 233 bp). The AY249982 repeat was almost a perfect match (92% nucleotide identity over 1018 bp) between 40,882 and 41,898 bp. Both these representatives of tandem repeat families were located within TEs, with the D30736 repetitive DNA sequence found within the CACTA DNA transposon <italic>Conan </italic>and the AY249982 tandem repeat found within the <italic>gypsy </italic>LTR retrotransposon <italic>Cereba</italic>.</p></sec><sec><title>Gene content annotation of <italic>ctg1034</italic></title><p>The 783,553 bp <italic>ctg1034 </italic>sequence was masked for repetitive elements with the repeat masking program Repeatmasker <ext-link ext-link-type="uri" xlink:href="http://www.repeatmasker.org">http://www.repeatmasker.org</ext-link> run using the triticeae repetitive element (TREP) database <ext-link ext-link-type="uri" xlink:href="http://wheat.pw.usda.gov/ITMI/Repeats">http://wheat.pw.usda.gov/ITMI/Repeats</ext-link>. The masked sequence was then passed through gene prediction programs FGENESH <ext-link ext-link-type="uri" xlink:href="http://linux1.softberry.com/berry.phtml">http://linux1.softberry.com/berry.phtml</ext-link> and GlimmerHMM [<xref ref-type="bibr" rid="B37">37</xref>]. Predicted gene models from both programs were screened against the Michigan State University (MSU) <italic>O. sativa </italic>annotation project's <ext-link ext-link-type="uri" xlink:href="http://rice.plantbiology.msu.edu/">http://rice.plantbiology.msu.edu/</ext-link> protein database and NCBI non-redundant amino-acid database using BLASTP to identify non-redundant gene matches. A database of 11,902 full-length wheat cDNA sequences from the KOMUGI Wheat Genetic Resource <ext-link ext-link-type="uri" xlink:href="http://www.shigen.nig.ac.jp/wheat/komugi/">http://www.shigen.nig.ac.jp/wheat/komugi/</ext-link> was also screened to identify any direct matches to wheat cDNAs. All annotated genes followed the standard GT-AG eukaryotic intron splice site model.</p><p>Four gene models of significant homology to characterised protein matches in NCBI non-redundant amino acid and MSU rice protein database were all found within a 16 kb window between 491,000-507,000 bp of the <italic>ctg1034 </italic>contig. The first gene model found at the very beginning of the 16 kb region was identified to be a fragment (28% coverage) of the MSU rice gene hit, LOC_Os05 g35160 (Clathrin assembly protein) with no significant wheat EST or cDNA match and was not considered further. The other three gene models were annotated as gene-coding sequences and all had hits to the NCBI non-redundant protein database. All three genes were annotated using BLASTX alignments to the MSU rice protein annotations [<xref ref-type="bibr" rid="B38">38</xref>] and their intron-exon structure was confirmed using both a wheat subset of Expressed Sequence Tags (ESTs) from NCBI and rice full-length cDNA information [<xref ref-type="bibr" rid="B39">39</xref>]. The overall gene-density of the <italic>ctg1034 </italic>sequence was 1 gene per 261,184 bp.</p><p>The first of the three genes, named <italic>TaEP1</italic>, was identified to be 2,489 bp in length and encoded a predicted protein of 551 amino acids over 2 exons (Table <xref ref-type="table" rid="T2">2</xref>). The gene has a high similarity at the amino acid level (85% identity) to an expressed protein in rice (LOC_Os01 g68830) as well as a catalytic domain-containing protein in Arabidopsis (<italic>Arabidopsis thaliana</italic>; At3 g07210) (49% identity). The gene was supported by multiple wheat full-length ESTs (CJ799192, BE500656, BG263254, BQ170023) all with a greater than 95% nucleotide identity. The second gene (<italic>TaCRP1</italic>) was quite small at only 436 bp in length and encoded a predicted protein of 118 amino acids over 2 exons (Table <xref ref-type="table" rid="T2">2</xref>). The gene was well supported by multiple full-length ESTs (CA636856, BQ806045, CA702257 and CA707955), which all had a greater than 95% nucleotide identity. The predicted protein of the gene was found to have homology (60% aminoacid identity)to an expressed protein in rice (LOC_Os01 g68840), which appears in the MSU rice community annotation as a small, cysteine-rich protein named <italic>CRP6</italic>[<xref ref-type="bibr" rid="B40">40</xref>]. In previous work involving legumes [<xref ref-type="bibr" rid="B41">41</xref>], small cysteine rich peptides (CRPs) were classified as different classes of defensins, proteins that are active in conferring resistance to bacteria, fungi and viruses. The Cx(2)-CxCCx(6)-Cx(4)-CCx(4)-Cx(9)-Cx(6)-CxCx(2) (Figure <xref ref-type="fig" rid="F3">3b</xref>) arrangement of the cysteine domain in <italic>TaCRP1</italic>corresponds to the ma ternally expressed gene (MEG) family.</p><fig id="F3" position="float"><label>Figure 3</label><caption><p><bold>Multiple sequence alignment of three collinear gene island genes (<italic>TaEP1 </italic>(A), <italic>TaCRP1 </italic>(B) and <italic>TaZFN1</italic>(C)) using CLUSTALX </bold>[<xref ref-type="bibr" rid="B78">78</xref>]. Each of the wheat, Brachypodium and maize genes were annotated in this study, while the <italic>S. bicolor </italic>(v1.0 annotations from <ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net/sorghum">http://www.phytozome.net/sorghum</ext-link>) and rice annotations [<xref ref-type="bibr" rid="B38">38</xref>]. Annotated on the <italic>TaCRP1 </italic>alignment is the signal peptide and cysteine-rich domain structures outlined in [<xref ref-type="bibr" rid="B40">40</xref>]. Colors found on the figure are determined by the CLUSTAL color scheme, which is based on amino acid types.</p></caption><graphic xlink:href="1471-2229-10-98-3"></graphic></fig><table-wrap id="T2" position="float"><label>Table 2</label><caption><p>Gene and EST analysis of the <italic>ctg1034</italic>'gene -island' genes</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center">Gene</th><th align="center">Position</th><th align="center">Size (bp)</th><th align="center">Number of exons</th><th align="center">Number of amino acids</th><th align="center">Wheat EST (>80% coverage)</th><th align="center">E-value</th><th align="center">Gene coverage</th><th align="center">Wheat Unigene set</th></tr></thead><tbody><tr><td align="center"><italic>TaEP1</italic></td><td align="center">493556-496044</td><td align="center">2489</td><td align="center">2</td><td align="center">551</td><td align="center">CJ799192 (667 bp)</td><td align="center">0.0</td><td align="center">27% (over 1 exon)</td><td align="center">Ta.11404</td></tr><tr><td align="center"><italic>TaCRP1</italic></td><td align="center">500300-500735</td><td align="center">436</td><td align="center">2</td><td align="center">118</td><td align="center">BQ806045 (623 bp)</td><td align="center">0.0</td><td align="center">73% (over 2 exons)</td><td align="center">Ta.14062</td></tr><tr><td align="center"><italic>TaZFN1</italic></td><td align="center">502241-506766</td><td align="center">4526</td><td align="center">7</td><td align="center">435</td><td align="center">CK209603 (1147 bp)</td><td align="center">7e-<sup>144</sup></td><td align="center">21% (over 5 exons)</td><td align="center">Ta.11131</td></tr></tbody></table></table-wrap><p>The last gene matched the NCBI non-redundant amino acid database was annotated as a zinc finger protein (<italic>TaZFN1</italic>). This gene was 4,525 bp, has a 7-exon gene structure and encodes a predicted protein of 430 amino acids (Table <xref ref-type="table" rid="T2">2</xref>). The gene was shown to have high homology (82% identity) to the rice zinc finger CCCH domain-containing protein ZFN-like 2 (Q5JLB5) and well supported by wheat ESTs (Table <xref ref-type="table" rid="T2">2</xref>) and a full-length wheat cDNA taken from the KOMUGI Wheat Genetic Resources Resource <ext-link ext-link-type="uri" xlink:href="http://www.shigen.nig.ac.jp/wheat/komugi/">http://www.shigen.nig.ac.jp/wheat/komugi/</ext-link>. <italic>TaZFN1 </italic>was the only one of the four identified gene models that had a match to a full-length wheat cDNA; the cDNA match to the coding sequence of <italic>TaZFN1 </italic>was almost 100%, with only 2 base differences.</p><p>The NCBI Unigene EST profiles <ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/unigene">http://www.ncbi.nlm.nih.gov/unigene</ext-link> of each of the genes were compared in Table <xref ref-type="table" rid="T3">3</xref>, showing the expression of each of the genes in wheat, barley (<italic>Hordeum vulgare</italic>) and rice tissue-specific EST pools. There was a low-level of transcription of the <italic>EP1 </italic>gene and no tissue specificity could be inferred from the data across all species. While there was a low-level of transcription found from the EST data for the <italic>CRP1 </italic>gene, there was clear seed-tissue specificity across all species relative to the expression in leaf and root tissues. The <italic>ZFN1 </italic>gene displayed much higher transcription levels than the previous two genes but like <italic>EP1 </italic>showed no tissue-specificity could be inferred.</p><table-wrap id="T3" position="float"><label>Table 3</label><caption><p>Wheat and Rice UniGene EST expression profiles of the three genes located within the <italic>ctg1034 </italic>gene island.</p></caption><table frame="hsides" rules="groups"><thead><tr><th></th><th align="center">UniGene Accession</th><th align="center">Seed*</th><th align="center">Leaf*</th><th align="center">Root*</th><th align="center">Stem*</th><th align="center">Callus*</th></tr></thead><tbody><tr><td align="center"><bold>EP1</bold></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td colspan="7"><hr></hr></td></tr><tr><td align="center">Wheat</td><td align="center">Ta.11404</td><td align="center"><bold>2 (21)</bold></td><td align="center"><bold>0</bold></td><td align="center"><bold>2 (11)</bold></td><td align="center"><bold>0</bold></td><td align="center"><bold>0</bold></td></tr><tr><td></td><td align="center">EST pool sizes</td><td align="center">161877</td><td align="center">57503</td><td align="center">166795</td><td align="center">93580</td><td align="center">10594</td></tr><tr><td align="center">Barley**</td><td align="center">Hv.27853</td><td align="center"><bold>0</bold></td><td align="center"><bold>1 (17)</bold></td><td align="center"><bold>0</bold></td><td align="center"><bold>0</bold></td><td align="center"><bold>0</bold></td></tr><tr><td></td><td align="center">EST pool sizes</td><td align="center">88535</td><td align="center">111884</td><td align="center">32853</td><td align="center">65681</td><td align="center">16046</td></tr><tr><td align="center">Rice</td><td align="center">Os.42759</td><td align="center"><bold>0</bold></td><td align="center"><bold>1 (5)</bold></td><td align="center"><bold>0</bold></td><td align="center"><bold>3 (23)</bold></td><td align="center"><bold>1 (6)</bold></td></tr><tr><td></td><td align="center">EST pool sizes</td><td align="center">32419</td><td align="center">171897</td><td align="center">68247</td><td align="center">126907</td><td align="center">164917</td></tr><tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td align="center"><bold>CRP1</bold></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td align="center">Wheat</td><td align="center">Ta.14062</td><td align="center">4 (24)</td><td align="center">0</td><td align="center">0</td><td align="center">0</td><td align="center">0</td></tr><tr><td align="center">Barley</td><td align="center">Hv.19960</td><td align="center">1 (11)</td><td align="center">0</td><td align="center">0</td><td align="center">1 (15)</td><td align="center">1 (62)</td></tr><tr><td align="center">Rice</td><td align="center">Os.65102</td><td align="center">3 (92)</td><td align="center">0</td><td align="center">0</td><td align="center">0</td><td align="center">8 (48)</td></tr><tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td align="center"><bold>ZFN1</bold></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td align="center">Wheat</td><td align="center">Ta.11131</td><td align="center">34 (210)</td><td align="center">8 (139)</td><td align="center">6 (35)</td><td align="center">11 (117)</td><td align="center">1 (94)</td></tr><tr><td align="center">Barley</td><td align="center">Hv.8311</td><td align="center">4 (45)</td><td align="center">11 (98)</td><td align="center">2 (60)</td><td align="center">2 (30)</td><td align="center">0</td></tr><tr><td align="center">Rice</td><td align="center">Os.19086</td><td align="center">3 (92)</td><td align="center">5 (29)</td><td align="center">0</td><td align="center">3 (23)</td><td align="center">12 (2)</td></tr></tbody></table><table-wrap-foot><p>*The number of tissue-specific ESTs is shown and the extrapolated transcripts per million (TPM) are shown in brackets</p><p>**Barley EST profiles are also shown on the basis of BLASTN homology searches against the NCBI EST dataset.</p></table-wrap-foot></table-wrap></sec><sec><title>Comparative analysis using the gene-island-coding sequences from cereal genomes</title><p>The three genes found as a small cluster or island within the wheat <italic>ctg1034 </italic>region of chromosome 3B were used to search against the rice (<italic>O. sativa ssp. japonica</italic>) and <italic>Sorghum bicolor </italic>genome sequences and each genome was found to be syntenic over the region, showing both conserved gene order and orientation. The rice MSU version 6 annotation of chromosome 1 between 39,898,000 to 40,011,000 bp (Table <xref ref-type="table" rid="T2">2</xref>) in the rice genome was used along with the <italic>Sorghum </italic>Sbi1.4 annotation models (from MIPS/PASA on v1.0 assembly preliminary Genome-scan annotation of assembly sbi0 <ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net">http://www.phytozome.net</ext-link>) from chromosome 3 of <italic>Sorghum bicolor </italic>from between 71,051,000 and 71,068,000 bp (17 kb region).</p><p>The three genes from <italic>ctg1034 </italic>were also searched against the Brachypodium (<italic>Brachypodium distachyon</italic>) line Bd21 and maize (<italic>Zea mays cv B73</italic>) genome sequences using BLASTN and the top hits of all three were once again found to have conserved gene order and orientation. The equivalent of the wheat 16 kb region in the draft Brachypodium super13 scaffold sequence (1311-1327 kb) contained the conserved colinear genes and was annotated using the same protocol used to annotate the <italic>ctg1034 </italic>wheat genome sequence. The three genes were named <italic>BdEP1</italic>, <italic>BdCRP1 </italic>and <italic>BdZFN1 </italic>based on their rice protein matches in the MSU version 6 annotations (same as the wheat gene annotation, Table <xref ref-type="table" rid="T4">4</xref>). A small genomic sequence gap within the draft sequence (4× sequence coverage) located inside exon 6 and intron 5 of <italic>BdZFN1 </italic>was filled on request to the Brachypodium genome-sequencing project (Bevan, M., pers. comm.) and reduced the size of the syntenic gene island sequence to 14 kb. A syntenic region containing the <italic>TaEP1</italic>, <italic>TaCRP1 </italic>and <italic>TaZFN1 </italic>genes in maize was located within the ctg131 FPC contig on maize chromosome 3. The maize genomic BAC clone containing all three genes (AC217295.3) was accessed from the maize genome sequence project website <ext-link ext-link-type="uri" xlink:href="http://maizesequence.org/">http://maizesequence.org/</ext-link> and were annotated for all genes (Additional file <xref ref-type="supplementary-material" rid="S1">1</xref>) based on alignments to <italic>Sorghum bicolor </italic>gene annotations <ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net/sorghum">http://www.phytozome.net/sorghum</ext-link> with intron-exon structures confirmed using NCBI maize ESTs. The three genes were named <italic>ZmEP1</italic>, <italic>ZmCRP1 </italic>and <italic>ZmZFN1</italic>. Transposable elements were annotated using BLASTN against the TIGR Zea repeat database [<xref ref-type="bibr" rid="B42">42</xref>](Figure S2 in Additional file <xref ref-type="supplementary-material" rid="S2">2</xref>).</p><table-wrap id="T4" position="float"><label>Table 4</label><caption><p>Characteristics of three wheat genes identified to be syntenic and colinear genome sequences to the rice, Brachypodium and <italic>S. bicolor </italic>genome sequences.</p></caption><table frame="hsides" rules="groups"><thead><tr><th></th><th></th><th align="center" colspan="2">Rice Genome</th><th align="center" colspan="2"><italic>S. bicolor </italic>Genome</th><th align="center" colspan="2">Maize Genome</th><th align="center" colspan="2">Brachypodium Genome</th></tr></thead><tbody><tr><td align="left"><bold>Gene</bold></td><td align="left"><bold>Description</bold></td><td align="left"><bold>Gene Match</bold></td><td align="left"><bold>Chr1 position (strand)</bold></td><td align="left"><bold>Gene Match</bold></td><td align="left"><bold>Chr3 position (strand)</bold></td><td align="left"><bold>Gene Match*</bold></td><td align="left"><bold>AC217295.3 Position (strand)</bold></td><td align="left"><bold>Gene Match*</bold></td><td align="left"><bold>Super_13 position (strand)</bold></td></tr><tr><td colspan="10"><hr></hr></td></tr><tr><td align="left"><italic>TaEP1</italic></td><td align="left">Expressed Protein</td><td align="left">LOC_Os01 g68830</td><td align="left">39991137-39993669 (+)</td><td align="left">Sb03 g043790</td><td align="left">71051976-71055103 (+)</td><td align="left"><italic>ZmEP1</italic></td><td align="left">65318-67814 (+)</td><td align="left"><italic>BdEP1</italic></td><td align="left">1312106-1314592 (+)</td></tr><tr><td align="left"><italic>TaCRP1</italic></td><td align="left">Expressed Protein</td><td align="left">LOC_Os01 g68840</td><td align="left">39997846-39997379(-)</td><td align="left">Sb03 g043800</td><td align="left">71059536-71060101(-)</td><td align="left"><italic>ZmCRP1</italic></td><td align="left">117899-118353 (-)</td><td align="left"><italic>BdCRP1</italic></td><td align="left">1317872-1318293 (-)</td></tr><tr><td align="left"><italic>TaZFN1</italic></td><td align="left">Putative zinc finger CCCH type <break></break>domain- containing protein</td><td align="left">LOC_Os01 g68860</td><td align="left">40009733-40005685 (-)</td><td align="left">Sb03 g043810</td><td align="left">71062164-71067135 (-)</td><td align="left"><italic>ZmZFN1</italic></td><td align="left">119558-125029 (-)</td><td align="left"><italic>BdZFN1</italic></td><td align="left">1319767-1324280 (-)</td></tr></tbody></table><table-wrap-foot><p>*denotes the Brachypodium and maize genes that were annotated along with wheat in this study.</p></table-wrap-foot></table-wrap><p><italic>TaEP1 </italic>showed the highest level of amino-acid conservation (Figure <xref ref-type="fig" rid="F3">3a</xref>) among the <italic>EP1 </italic>genes in the cereal genomes. The highest similarity was with Brachypodium <italic>BdEP1 </italic>(88% identity at the amino acid level), followed by rice LOC_Os01 g68830 (85%), <italic>S. bicolor </italic>Sb03 g043790 and maize <italic>ZmEP1 </italic>(both 81% identity). <italic>TaEP1 </italic>also had 49% amino acid identity to a peptidase protein AT3G07210 in Arabidopsis. The Brachypodium <italic>BdEP1 </italic>also had a good conservation of non-coding nucleotide sequence within the intron of <italic>TaEP1</italic>. The intron sequence of <italic>BdEP1 </italic>was 70% identical over 836 nucleotides with 85% sequence coverage compared to the rice comparison, which had only 16% coverage over the 826 nucleotides. There was a small region of 110 bp near the start of the intron that did not show any homology. The intron sequence of maize <italic>ZmEP1 </italic>compared to <italic>S. bicolor </italic>Sb03 g043790 was also highly conserved (78% identical over 821 nucleotides with 99% coverage).</p><p>The large 7-exon <italic>TaZFN1 </italic>gene, much like <italic>TaEP1</italic>, showed significant homology to its Brachypodium orthologous sequence. The amino acid sequences of both genes showed 89% identity over 387 amino acids, with only a small section located within the first exon lacking homology. Both <italic>S. bicolor </italic>(403 amino acids) and rice (443 amino acids) showed 82% identity compared to <italic>TaZFN1</italic>, with maize showing the least similarity at amino acid level (77% over 429 amino acids). The amino acids from the first exon (1-80 amino acids in Figure <xref ref-type="fig" rid="F3">3c</xref>) seemed to contain the most sequence divergence when compared to the rest of the genome sequences. As was found in <italic>TaEP1</italic>, there was a significant conservation of the non-coding sequence between <italic>TaZFN1 </italic>and <italic>BdZFN1</italic>, especially in introns 3, 5 and 6 which all have a nucleotide sequence coverage of >62%. The <italic>ZFN1 </italic>gene sequence between maize and <italic>S. bicolor </italic>was also well conserved (84% identity over 4915 nucleotides) except for two small inserts contained within the fifth intron of <italic>ZmZFN1</italic>, one insert of 1,166 bp and another of 118 bp. The larger 1,166 bp insert contained two small transposable elements <italic>CASINE </italic>(63 bp) and <italic>F524 </italic>(91 bp) classified as SINE elements from the non-LTR retrotransposable element group.</p><p>By comparison, the <italic>TaCRP1 </italic>showed the least amount of homology across the genomes when analysed at the amino acid level (Figure <xref ref-type="fig" rid="F3">3b</xref>) relative to <italic>TaEP1 </italic>and <italic>TaZFN1</italic>. Once again, Brachypodium had the highest amino acid homology (85% identity), followed by rice (66%), <italic>S. bicolor </italic>(62%) and maize (60%). The low amino acid identity was due to insertions within the rice, maize and <italic>S. bicolor </italic>amino acid sequences. <italic>S. bicolorSb03 g043800 </italic>had a 33 amino acid insertion located just after the signal peptide and before the cysteine domain. It is also the only <italic>CRP1 </italic>sequence out of the five syntenic gene copies that had only one exon (no intron). The cysteine domain located in the last 50 amino acids of the gene was conserved in all genomes (~75% identity). The only significant difference in the cysteine-rich domain across all genomes was a six amino acid insertion (all glycine residues) within the rice LOC_Os01 g68840 sequence. Exon 1 in all sequences that contained multiple exons showed little nucleotide and amino acid sequence homology and exon 2 was the only region found to have significant sequence conservation. Exon 2 contained the coding sequence of the cysteine-rich domain. No significant intron sequence similarity could be identified across the genomes.</p></sec><sec><title>The syntenic gene island region across five genomes</title><p>The <italic>ctg1034 </italic>14 kb gene island was analysed across the available genomic sequences including Arabidopsis genome sequence [<xref ref-type="bibr" rid="B43">43</xref>], the grapevine (<italic>Vitis vinifera</italic>) genome sequence [<xref ref-type="bibr" rid="B44">44</xref>] and the wheat, Brachypodium, <italic>S. bicolor</italic>, rice and maize genome sequences. The 14 kb, three-gene region containing <italic>TaEP1</italic>, <italic>TaCRP1 </italic>and <italic>TaZFN1 </italic>did not show any conservation of colinearity in the Arabidopsis genome sequence. Chromosome 4 of the grapevine genome did have homologs of <italic>TaCRP1 </italic>and <italic>TaZFN1 </italic>located within a 17 kb window (in the same relative orientation as in wheat) but also contained a small (65 predicted amino acid) gene found in between. This small gene coding for a 65 aa protein has no rice or Arabidopsis BLASTX hit and could possibly be within a transposable element.</p><p>There are large size differences of the gene-island regions between wheat (16 kb) and both maize (63 kb) and rice (22 kb) resulted from an insertion-deletion event (InDel) in both cases. Comparing the genome sequences of rice against the wheat gene island region shows a 6-7 kb sequence variation (InDel) between the <italic>OsCRP1 </italic>and <italic>OsZFN1 </italic>genes (Figure <xref ref-type="fig" rid="F4">4</xref>). The proposed InDel within the rice genome contains a hypothetical protein annotation LOC_Os01 g68850 and contained many MITE and DNA transposons found in the TIGR Oryza Repeat Database v3.1 (repeat_212948; 230577; 212949; 205504; 216962) including a MULE or Mutator-like element (BPM2_1011). The LOC_Os01 g68850 open-reading frame was identified using FGENESH and contained a high amount of repetitive elements. Furthermore, the match to sequences in the EST databases of rice indicated the largest region of significant homology (94% identity to rice EST CK043734) was only 208 bp and thus it seems unlikely to be an active entity.</p><fig id="F4" position="float"><label>Figure 4</label><caption><p><bold>Pair-wise sequence comparison of wheat and Brachypodium gene island regions against the wheat and rice gene island regions</bold>. The wheat genes (<italic>TaEP1</italic>, <italic>TaCRP1 </italic>and <italic>TaZFN1</italic>) are annotated on the figure and the arrows indicate the proposed insertion-deletion (InDel) events resulting in sequence movement between the species. Wheat contained a ~500 bp InDel, while Brachypodium and rice showed ~200 bp and ~6-7 kb InDels respectively.</p></caption><graphic xlink:href="1471-2229-10-98-4"></graphic></fig><p>Overall, in five of the genome sequences used in this study, there was a highly conserved gene sequence, order and orientation, when compared to the wheat <italic>ctg1034 </italic>gene island (Figure <xref ref-type="fig" rid="F5">5</xref>), even though the size of the region differed considerably; greatest in the maize genome (63 kb), followed by rice (22 kb), <italic>S. bicolor </italic>(17 kb) and Brachypodium (14 kb) (Figure <xref ref-type="fig" rid="F5">5</xref>). The 4× draft Brachypodium super13 scaffold sequence showed the highest nucleotide coverage (53% coverage), followed by rice (31%), <italic>S. bicolor </italic>(29%) and maize (23%) when each sequence was compared to the 16 kb gene island wheat genomic sequence using NCBI BLAST 2 Sequences (BLASTN) [<xref ref-type="bibr" rid="B45">45</xref>]. A detailed analysis of the differences in length in this region between the genomes analysed (Figure <xref ref-type="fig" rid="F4">4</xref> and the red triangles in Figure <xref ref-type="fig" rid="F5">5</xref>) is provided in the Additional file <xref ref-type="supplementary-material" rid="S2">2</xref>.</p><fig id="F5" position="float"><label>Figure 5</label><caption><p><bold>A gene island sequence summary figure next to a deduced evolutionary tree from analysed genome sequences homologous to the wheat chromosome 3BL <italic>ctg1034 </italic>gene island</bold>. The red triangles indicate proposed insertion-deletion (InDel) events identified in this study. An example of a dot plot indicating the occurrence of InDels is shown beneath the pair-wise sequence comparison between the maize and <italic>S. bicolor</italic>. The analysis demonstrates the location of the InDels between the start of the cysteine-rich peptide gene (<italic>CRP1</italic>) to the end of the Zinc finger protein (<italic>ZFN1</italic>) region. A detailed analysis of the differences in length in this region between the genomes analysed (red triangles) is provided in the Additional file <xref ref-type="supplementary-material" rid="S2">2</xref>.</p></caption><graphic xlink:href="1471-2229-10-98-5"></graphic></fig></sec></sec><sec><title>Discussion</title><p>In this study a group of twelve hexaploid wheat (<italic>Triticum aestivum </italic>cv Chinese Spring) BAC clones from chromosome 3B were assembled into a 783,553 bp genomic sequence (called <italic>ctg1034</italic>) that was then analysed for biological features.</p><sec><title>Diverse gene functions in a conserved gene-island</title><p>The three gene-coding sequences on <italic>ctg1034 </italic>(<italic>TaEP1</italic>, <italic>TaCRP1 </italic>and <italic>TaZFN1</italic>), located within a 14 kb sequence, all show different sequence characteristics and a range of expression patterns and functions based on rice annotations. <italic>TaEP1 </italic>is highly conserved in plant genomes (even in Arabidopsis) but does not show any distinct characterised function in sequenced genomes such as <italic>S. bicolor </italic>and rice. <italic>TaCRP1</italic>, on the other hand, is a small cysteine-rich protein, a protein from a diverse, well characterised protein family that is involved in pathogen defence [<xref ref-type="bibr" rid="B40">40</xref>]. <italic>TaZFN1 </italic>was like <italic>TaCRP1</italic>, a well-characterised protein from a large family of transcription factors that have been extensively studied. Furthermore multiple full-length cDNA sequences of <italic>TaZFN1 </italic>in rice indicate alternative splicing forms of the gene product (LOC_Os01 g68860.1, LOC_Os01 g68860.2 and LOC_Os01 g68860.3) exist. EST expression profiles from 3 did not provide any clear indication of co-expression of the three genes; <italic>TaZFN1 </italic>was striking in its relatively high levels of expression in a range of tissue compared to <italic>TaEP1 </italic>and <italic>TaCRP1</italic>. This is consistent with the genes being involved in independent pathways within cells.</p></sec><sec><title>Gene island structure is maintained over the evolution of plant genomes despite the occurrence of InDels</title><p>Conservation of colinearity between grass species has been reported extensively at a micro-level [<xref ref-type="bibr" rid="B17">17</xref>,<xref ref-type="bibr" rid="B46">46</xref>] but even in colinear regions, gene order and orientation may not be conserved [<xref ref-type="bibr" rid="B6">6</xref>,<xref ref-type="bibr" rid="B9">9</xref>,<xref ref-type="bibr" rid="B17">17</xref>,<xref ref-type="bibr" rid="B46">46</xref>-<xref ref-type="bibr" rid="B48">48</xref>]. The conserved gene-islands described between wheat and other major crop species such as rice [<xref ref-type="bibr" rid="B11">11</xref>], have been limited because of the use of EST and single BAC sequences (unlike the large assembled sequences created in this study), with the associated lack resolution making it difficult to reach definitive conclusions about the level of conservation. While conserved gene islands at gene-rich orthologous loci have been shown, small genetic rearrangements were found to dramatically change gene order in maize and <italic>S. bicolor </italic>[<xref ref-type="bibr" rid="B48">48</xref>] and a mosaic of rearrangements between rice and wheat were also reported, with the conservation of gene orientation only limited to local duplications in one species [<xref ref-type="bibr" rid="B49">49</xref>].</p><p>The gene island provides a contrast to the concepts developing from mammalian genome studies that repeat sequence regions may be hot-spots for structural change in gene regions [<xref ref-type="bibr" rid="B50">50</xref>]. While the relative order and orientation of the genes within the <italic>ctg1034 </italic>gene island has been maintained, the intergenic region was not immune to changes during the course of its evolution. Figure <xref ref-type="fig" rid="F5">5</xref> shows a summary evolutionary tree deduced from colinearity and sequence similarity seen in this study over the <italic>ctg1034 </italic>gene island. This evolutionary tree is consistent with taxonomic relationships [<xref ref-type="bibr" rid="B51">51</xref>].</p><p>Despite the large amount of repetitive elements that surround the island, only the rice and maize genome (Figure <xref ref-type="fig" rid="F5">5</xref> and Additional file <xref ref-type="supplementary-material" rid="S2">2</xref>) sequences showed post-divergence TE insertions. An insert within maize is not unusual, as [<xref ref-type="bibr" rid="B52">52</xref>] has shown that even maize inbred lines can show intra-specific variation in genetic colinearity. High sequence diversity in maize can be caused by TEs such as <italic>Helitrons </italic>[<xref ref-type="bibr" rid="B52">52</xref>-<xref ref-type="bibr" rid="B54">54</xref>]. The 6-7 kb rice insertion mostly contained miniature inverted TEs (MITEs), known to insert into and be associated with gene-containing regions [<xref ref-type="bibr" rid="B23">23</xref>,<xref ref-type="bibr" rid="B55">55</xref>,<xref ref-type="bibr" rid="B56">56</xref>] and [<xref ref-type="bibr" rid="B36">36</xref>] suggested that these small TEs might also have a role in modification of expression in neighbouring genes. Another TE found within the insert was a <italic>MULE </italic>transposon. So called <italic>Pack-MULEs </italic>are extremely common in the rice genome [<xref ref-type="bibr" rid="B57">57</xref>] and have been implicated in the evolution of genes within higher plant genomes through their ability to capture and carry fragments of genomic DNA to create new open reading frames.</p></sec><sec><title>Gene island location on chromosome 3BL</title><p>The gene density in this study was identified to be quite low at 1 gene per 260 kb. In contrast, gene densities in <italic>Triticeae </italic>genomes (most notably barley and wheat) have been reported to be much higher (1 gene per 9 kb [<xref ref-type="bibr" rid="B58">58</xref>] and 1 gene per 4-5 kb [<xref ref-type="bibr" rid="B19">19</xref>]), possibly reflecting the initial targeting of important agronomic genes in distal regions of chromosomes [<xref ref-type="bibr" rid="B59">59</xref>] rather than a random representation of the genome sequence. Random wheat BAC sequencing [<xref ref-type="bibr" rid="B7">7</xref>] indicated that even in gene-rich regions of wheat, the gene density is considerably lower than previously thought (approximately 1 gene per 75 kb). Genetic mapping studies showed Sc3-119 and Sc3-120 ISBP markers from <italic>ctg1034 </italic>were located within the terminal deletion bin 3BL-7 on chromosome 3B (Figure <xref ref-type="fig" rid="F2">2</xref>), a deletion bin known to contain two major C-bands [<xref ref-type="bibr" rid="B59">59</xref>]. Previous cytogenetic studies of the wheat chromosomes suggested a large variation of gene-density over the entire length of chromosomes [<xref ref-type="bibr" rid="B60">60</xref>,<xref ref-type="bibr" rid="B61">61</xref>] and it is feasible that particularly low gene densities occur within C band regions. The low gene density found in this study is more consistent with studies in <italic>Triticeae </italic>genomes of more proximal regions of chromosome arms (1 gene per 518 kb [<xref ref-type="bibr" rid="B62">62</xref>]) and regions of low recombination (1 gene per 175 kb [<xref ref-type="bibr" rid="B63">63</xref>]).</p><p>The two representatives of tandem repeat families located within the first 75 kb of the <italic>ctg1034 </italic>sequence also indicate a relationship to heterochromatin, with one (AY249982) being previously identified to be a D-genome centromeric heterochromatin tandem repeat sequence [<xref ref-type="bibr" rid="B35">35</xref>,<xref ref-type="bibr" rid="B36">36</xref>]. The presence of a representative of this D-genome specific repeat in the chromosome 3B sequence suggest specific amplification of the sequence family must have occurred in the D genome even though single copy representatives were located elsewhere. The presence of representatives of sequences normally located as tandem arrays in heterochromatin and the presence of high <italic>gypsy </italic>LTR content support our proposal that this <italic>ctg1034 </italic>genomic sequence is located within a C-banding region in deletion bin 7 of chromosome 3BL.</p><p>The highly repetitive element content in <italic>ctg1034 </italic>(81.81%) was not unusual in wheat sequences, as studies have shown repetitive element contents of greater than 70% [<xref ref-type="bibr" rid="B21">21</xref>,<xref ref-type="bibr" rid="B56">56</xref>,<xref ref-type="bibr" rid="B64">64</xref>], however the high content of the <italic>gypsy-like </italic>LTR retrotransposon is significant in this study (>50% of the entire contig). A previously sequenced wheat BAC clone from the same chromosome 3BL-7 deletion bin [<xref ref-type="bibr" rid="B5">5</xref>] also found a similar high proportion of <italic>gypsy-like </italic>LTR-retrotransposons. In the present study, chromodomains were shown to be located within the internal polyprotein domain of two <italic>gypsy</italic>-LTR retrotransposons, and are thus potentially key components defining the condensed nature of heterochromatin [<xref ref-type="bibr" rid="B29">29</xref>,<xref ref-type="bibr" rid="B65">65</xref>]. One of the potential chromodomains (<italic>Latidu </italic>LTR <italic>gypsy </italic>retrotransposon) was located immediately adjacent to the gene island in <italic>ctg1034</italic>.</p><p>The unusual properties of heterochromatin that would contribute to the unique conservation of both the gene order and relative gene orientation found in this study include: (a) the low levels of recombination and gene activity associated with heterochromatin [<xref ref-type="bibr" rid="B33">33</xref>,<xref ref-type="bibr" rid="B66">66</xref>]; (b) the high level of transcript processing by the RNAi machinery that mediates chromatin structure [<xref ref-type="bibr" rid="B67">67</xref>-<xref ref-type="bibr" rid="B71">71</xref>]. These properties could contribute to the relative isolation of the gene island from the normal processes that lead to genome rearrangements.</p></sec></sec><sec><title>Conclusion</title><p>BAC shotgun sequencing of the FPC physical map contig <italic>ctg1034 </italic>from the genome of chromosome 3B has provided the largest assembly of a wheat genome region to date (783,553 bp). Annotation and comparative analysis with four other plant genomes of (<italic>B. distachyon</italic>, <italic>O. sativa</italic>, <italic>S. bicolor </italic>and <italic>Zea mays</italic>) identified an island of three genes showing complete conservation of gene order and orientation. This conservation could not be readily accounted for by shared functions between the genes and it is proposed that <italic>ctg1034 </italic>is located within a heterochromatic C-band region of deletion bin 3BL7 based on the identification of representatives of heterochromatin tandem repeats and presence of significant matches to chromodomain-containing <italic>gypsy </italic>LTR retrotransposable elements. We speculate that this location, among other highly repetitive sequences, may account for the relative stability of the gene island through insulating the gene island from normal recombination processes.</p></sec><sec sec-type="methods"><title>Methods</title><sec><title>Mapping of selected BAC clones</title><p>Selected clones were mapped to chromosome 3B using insertion site based polymorphism (ISBP) markers [<xref ref-type="bibr" rid="B7">7</xref>,<xref ref-type="bibr" rid="B23">23</xref>]. Two ISBPs (Sc3-119 and Sc3-120) from <italic>ctg1034 </italic>were located on the long arm of chromosome 3B using standard deletion stocks of wheat [<xref ref-type="bibr" rid="B2">2</xref>]. The Sc3-119 primer 5'-TCCAAGACGTTTCTTCCACC-3' and 5'-GAGGTGACGTGGCATCATTA-3' generated a 158 bp product and was located at 510,455 bp within the <italic>ctg1034 </italic>sequence. The second ISBP used, Sc3-120 with primer '5-GCCCCTGGCTTGTATTATGA-3' and 5'-TCAGCTGAAGGGTCGTTTTT-3' giving a 190 bp specific fragment located at 523,485 bp. The PCRs carried out on genome DNA from the standard 3B deletion stocks and the 162 double haploid lines from the cross Cranbook × Halberd followed standard reaction conditions [<xref ref-type="bibr" rid="B25">25</xref>,<xref ref-type="bibr" rid="B72">72</xref>].</p></sec><sec><title>BAC shotgun sequencing</title><p><italic>E. coli</italic>-freed DNA from BAC clones was extracted with Qiagen Large-Construct Kit (QIAGEN, Cat. No. 20021) and mechanically sheared with HydroShear as recommended by ABI applied biosystems <ext-link ext-link-type="uri" xlink:href="https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=604432">https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID = 604432</ext-link>, generating a concentrated smear ~3-5 kb in length. The sheared fragments were blunt ended with mung bean nuclease and dephosphorylated with Shrimp Alkaline Phosphatase (SAP). The short fragments were then tailed with A by PCR using standard procedures.. Fragments ranging from 3-5 kb in size were isolated and ligated into a pCR4-TOPO vector and transformed into TOP10 electrocompetent cells (Invitrogen, Cat. No. K4580-01). The clones were sequenced from both directions with T3 and T7 primers using BigDye3.1 termination chemistry and run on an ABI Prism 3730 XL capillary sequencer (Applied Biosystems, Foster City, Calif., USA). Base calling, quality assessment and sequence assembly were done using the PHRED/PHRAP software package [<xref ref-type="bibr" rid="B23">23</xref>]. Gaps were filled by primer walking using adding dGTP mix and DMSO in the sequencing reaction system.</p></sec><sec><title>Sequence Analysis and Annotation</title><p>Repetitive DNA analysis was carried out using Repeatmasker (Smit et al. 1996-2004, <ext-link ext-link-type="uri" xlink:href="http://www.repeatmasker.org">http://www.repeatmasker.org</ext-link>) and BLAST local alignment searching [<xref ref-type="bibr" rid="B26">26</xref>] against the Triticeae repetitive element (TREP) database <ext-link ext-link-type="uri" xlink:href="http://wheat.pw.usda.gov/ITMI/Repeats/">http://wheat.pw.usda.gov/ITMI/Repeats/</ext-link> and the <italic>gypsy </italic>mobile elements database (GyDB) [<xref ref-type="bibr" rid="B34">34</xref>]. Open reading frames were identified by the use of FGENESH <ext-link ext-link-type="uri" xlink:href="http://www.softberry.com/">http://www.softberry.com/</ext-link>, GENSCAN [<xref ref-type="bibr" rid="B73">73</xref>] and GlimmerHMM [<xref ref-type="bibr" rid="B37">37</xref>]. Sequence homology searching was carried out by BLAST programs with a cut-off E-value of 1e<sup>-30 </sup>for nucleotide sequences and 1e<sup>-10 </sup>for amino acid sequences. All EST matches to genes were required to have >80% coverage over the EST sequence. Protein domains were identified by searching the Pfam protein family database [<xref ref-type="bibr" rid="B74">74</xref>], as well as the conserved domains database (CDD) at NCBI [<xref ref-type="bibr" rid="B75">75</xref>]. InterProScan [<xref ref-type="bibr" rid="B76">76</xref>] was run against the InterPro protein domain database [<xref ref-type="bibr" rid="B77">77</xref>], which also includes a signal peptide and Trans-membrane search. Pair-wise sequence comparisons were carried out using DOTTER [<xref ref-type="bibr" rid="B27">27</xref>] and multiple sequence comparisons were carried out using the CLUSTALX [<xref ref-type="bibr" rid="B78">78</xref>]. The hidden markov model search program HMMer [<xref ref-type="bibr" rid="B30">30</xref>] was also used. Graphical display of the sequence map was produced with WICKERsoft™ scripts.</p></sec><sec><title>Comparative Sequence analysis</title><p>Genome sequence annotations used in this study include release 5 of the TIGR rice pseudomolecules [<xref ref-type="bibr" rid="B38">38</xref>], the 4× draft genome sequence of <italic>B.distachyon </italic><ext-link ext-link-type="uri" xlink:href="http://www.brachypodium.org/">http://www.brachypodium.org/</ext-link>, the 2a.50 release of the Maize (<italic>Z. mays</italic>) genome sequence <ext-link ext-link-type="uri" xlink:href="http://www.maizesequence.org">http://www.maizesequence.org</ext-link> and release 1 of the <italic>S. bicolor </italic>genome <ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net/sorghum">http://www.phytozome.net/sorghum</ext-link>. Multipipmaker [<xref ref-type="bibr" rid="B79">79</xref>] and Multidotter [<xref ref-type="bibr" rid="B80">80</xref>] were used for nucleotide sequence comparisons. CLUSTALX was used to compare amino acid sequences and Multidotter, Mauve [<xref ref-type="bibr" rid="B81">81</xref>] and ACT [<xref ref-type="bibr" rid="B82">82</xref>] was used to compare multiple genome sequences at one time.</p></sec></sec><sec><title>Authors' contributions</title><p>All authors read and approved the final manuscript.</p><p>JB, TW, MB, RAs: Assembly of the genome sequence and annotation of genes and TEs</p><p>EP, CF: Cloning and assembly of BACs from chromosome 3B</p><p>XK, JZ: Sequencing of BAC clones</p><p>WM: Mapping of ISBPs to wheat genetic map</p></sec><sec sec-type="supplementary-material"><title>Supplementary Material</title><supplementary-material content-type="local-data" id="S1"><caption><title>Additional file 1</title><p><bold>Supplementary Table S1</bold>. Gene Annotation of Maize Chromosome 3 BAC AC217295.3.</p></caption><media xlink:href="1471-2229-10-98-S1.PDF" mimetype="application" mime-subtype="pdf"><caption><p>Click here for file</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="S2"><caption><title>Additional file 2</title><p><bold>Supplementary INDELs file</bold>. Detailed of the InDels shown as red triangles in Figures <xref ref-type="fig" rid="F4">4</xref> and <xref ref-type="fig" rid="F5">5</xref> of the main manuscript.</p></caption><media xlink:href="1471-2229-10-98-S2.PDF" mimetype="application" mime-subtype="pdf"><caption><p>Click here for file</p></caption></media></supplementary-material></sec></body><back><sec><title>Acknowledgements</title><p>The BAC clones used in this study derived from the Minimal Tiling Path of <italic>ctg1034 </italic>in the chromosome 3B physical map of hexaploid wheat project within the International Wheat Genome Sequencing Consortium (IWGSC). The authors thank Fred Choulet provided the <italic>Perl </italic>scripts for identifying ISBP markers. Thanks to Yasunari Ogihara(Kihara Institute for Biological Research and Graduate School of Integrated Science, Yokohama City University, Japan) for advanced access to full-length cDNAs for wheat and Junhong Ma (SABC, Murdoch University, Australia) for laboratory work. The authors appreciated the help provided by Prof M Bevan to fill-in a gap in the Brachypodium genome sequence. Finally, thanks to David Dunn, Paula Moolhuijzen and all technical staff at the CCG for Bioinformatics support. Molecular Plant Breeding Co-operative Research Centre (MPBCRC) and Murdoch University generously supported funding for this work.</p></sec><ref-list><ref id="B1"><mixed-citation publication-type="other"><name><surname>Gupta</surname><given-names>PK</given-names></name><name><surname>Mir</surname><given-names>RR</given-names></name><name><surname>Mohan</surname><given-names>A</given-names></name><name><surname>Kumar</surname><given-names>J</given-names></name><article-title>Wheat genomics: present status and future prospects</article-title><source>International journal of plant genomics</source><volume>2008</volume><fpage>896451</fpage><pub-id pub-id-type="pmid">18528518</pub-id></mixed-citation></ref><ref id="B2"><mixed-citation publication-type="journal"><name><surname>Gill</surname><given-names>BS</given-names></name><name><surname>Appels</surname><given-names>R</given-names></name><name><surname>Botha-Oberholster</surname><given-names>AM</given-names></name><name><surname>Buell</surname><given-names>CR</given-names></name><name><surname>Bennetzen</surname><given-names>JL</given-names></name><name><surname>Chalhoub</surname><given-names>B</given-names></name><name><surname>Chumley</surname><given-names>F</given-names></name><name><surname>Dvorak</surname><given-names>J</given-names></name><name><surname>Iwanaga</surname><given-names>M</given-names></name><name><surname>Keller</surname><given-names>B</given-names></name><etal></etal><article-title>A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium</article-title><source>Genetics</source><year>2004</year><volume>168</volume><fpage>1087</fpage><lpage>1096</lpage><pub-id pub-id-type="doi">10.1534/genetics.104.034769</pub-id><pub-id pub-id-type="pmid">15514080</pub-id></mixed-citation></ref><ref id="B3"><mixed-citation publication-type="journal"><name><surname>Wicker</surname><given-names>T</given-names></name><name><surname>Zimmermann</surname><given-names>W</given-names></name><name><surname>Perovic</surname><given-names>D</given-names></name><name><surname>Paterson</surname><given-names>AH</given-names></name><name><surname>Ganal</surname><given-names>M</given-names></name><name><surname>Graner</surname><given-names>A</given-names></name><name><surname>Stein</surname><given-names>N</given-names></name><article-title>A detailed look at 7 million years of genome evolution in a 439 kb contiguous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats</article-title><source>Plant J</source><year>2005</year><volume>41</volume><fpage>184</fpage><lpage>194</lpage><pub-id pub-id-type="doi">10.1111/j.1365-313X.2004.02285.x</pub-id><pub-id pub-id-type="pmid">15634196</pub-id></mixed-citation></ref><ref id="B4"><mixed-citation publication-type="journal"><name><surname>Paux</surname><given-names>E</given-names></name><name><surname>Sourdille</surname><given-names>P</given-names></name><name><surname>Salse</surname><given-names>J</given-names></name><name><surname>Saintenac</surname><given-names>C</given-names></name><name><surname>Choulet</surname><given-names>F</given-names></name><name><surname>Leroy</surname><given-names>P</given-names></name><name><surname>Korol</surname><given-names>A</given-names></name><name><surname>Michalak</surname><given-names>M</given-names></name><name><surname>Kianian</surname><given-names>S</given-names></name><name><surname>Spielmeyer</surname><given-names>W</given-names></name><etal></etal><article-title>A physical map of the 1-gigabase bread wheat chromosome 3B</article-title><source>Science</source><year>2008</year><volume>322</volume><fpage>101</fpage><lpage>104</lpage><pub-id pub-id-type="doi">10.1126/science.1161847</pub-id><pub-id pub-id-type="pmid">18832645</pub-id></mixed-citation></ref><ref id="B5"><mixed-citation publication-type="journal"><name><surname>Charles</surname><given-names>M</given-names></name><name><surname>Belcram</surname><given-names>H</given-names></name><name><surname>Just</surname><given-names>J</given-names></name><name><surname>Huneau</surname><given-names>C</given-names></name><name><surname>Viollet</surname><given-names>A</given-names></name><name><surname>Couloux</surname><given-names>A</given-names></name><name><surname>Segurens</surname><given-names>B</given-names></name><name><surname>Carter</surname><given-names>M</given-names></name><name><surname>Huteau</surname><given-names>V</given-names></name><name><surname>Coriton</surname><given-names>O</given-names></name><etal></etal><article-title>Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat</article-title><source>Genetics</source><year>2008</year><volume>180</volume><fpage>1071</fpage><lpage>1086</lpage><pub-id pub-id-type="doi">10.1534/genetics.108.092304</pub-id><pub-id pub-id-type="pmid">18780739</pub-id></mixed-citation></ref><ref id="B6"><mixed-citation publication-type="journal"><name><surname>Dubcovsky</surname><given-names>J</given-names></name><name><surname>Ramakrishna</surname><given-names>W</given-names></name><name><surname>SanMiguel</surname><given-names>PJ</given-names></name><name><surname>Busso</surname><given-names>CS</given-names></name><name><surname>Yan</surname><given-names>L</given-names></name><name><surname>Shiloff</surname><given-names>BA</given-names></name><name><surname>Bennetzen</surname><given-names>JL</given-names></name><article-title>Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes</article-title><source>Plant Physiol</source><year>2001</year><volume>125</volume><fpage>1342</fpage><lpage>1353</lpage><pub-id pub-id-type="doi">10.1104/pp.125.3.1342</pub-id><pub-id pub-id-type="pmid">11244114</pub-id></mixed-citation></ref><ref id="B7"><mixed-citation publication-type="journal"><name><surname>Devos</surname><given-names>KM</given-names></name><name><surname>Ma</surname><given-names>J</given-names></name><name><surname>Pontaroli</surname><given-names>AC</given-names></name><name><surname>Pratt</surname><given-names>LH</given-names></name><name><surname>Bennetzen</surname><given-names>JL</given-names></name><article-title>Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat</article-title><source>Proc Natl Acad Sci USA</source><year>2005</year><volume>102</volume><fpage>19243</fpage><lpage>19248</lpage><pub-id pub-id-type="doi">10.1073/pnas.0509473102</pub-id><pub-id pub-id-type="pmid">16357197</pub-id></mixed-citation></ref><ref id="B8"><mixed-citation publication-type="journal"><name><surname>Dubcovsky</surname><given-names>J</given-names></name><name><surname>Dvorak</surname><given-names>J</given-names></name><article-title>Genome plasticity a key factor in the success of polyploid wheat under domestication</article-title><source>Science</source><year>2007</year><volume>316</volume><fpage>1862</fpage><lpage>1866</lpage><pub-id pub-id-type="doi">10.1126/science.1143986</pub-id><pub-id pub-id-type="pmid">17600208</pub-id></mixed-citation></ref><ref id="B9"><mixed-citation publication-type="journal"><name><surname>Appels</surname><given-names>R</given-names></name><name><surname>Francki</surname><given-names>M</given-names></name><name><surname>Chibbar</surname><given-names>R</given-names></name><article-title>Advances in cereal functional genomics</article-title><source>Funct Integr Genomics</source><year>2003</year><volume>3</volume><fpage>1</fpage><lpage>24</lpage><pub-id pub-id-type="pmid">12590339</pub-id></mixed-citation></ref><ref id="B10"><mixed-citation publication-type="journal"><name><surname>Yan</surname><given-names>L</given-names></name><name><surname>Loukoianov</surname><given-names>A</given-names></name><name><surname>Tranquilli</surname><given-names>G</given-names></name><name><surname>Helguera</surname><given-names>M</given-names></name><name><surname>Fahima</surname><given-names>T</given-names></name><name><surname>Dubcovsky</surname><given-names>J</given-names></name><article-title>Positional cloning of the wheat vernalization gene VRN1</article-title><source>Proc Natl Acad Sci USA</source><year>2003</year><volume>100</volume><fpage>6263</fpage><lpage>6268</lpage><pub-id pub-id-type="doi">10.1073/pnas.0937399100</pub-id><pub-id pub-id-type="pmid">12730378</pub-id></mixed-citation></ref><ref id="B11"><mixed-citation publication-type="journal"><name><surname>Sorrells</surname><given-names>ME</given-names></name><name><surname>La Rota</surname><given-names>M</given-names></name><name><surname>Bermudez-Kandianis</surname><given-names>CE</given-names></name><name><surname>Greene</surname><given-names>RA</given-names></name><name><surname>Kantety</surname><given-names>R</given-names></name><name><surname>Munkvold</surname><given-names>JD</given-names></name><name><surname>Miftahudin</surname></name><name><surname>Mahmoud</surname><given-names>A</given-names></name><name><surname>Ma</surname><given-names>X</given-names></name><name><surname>Gustafson</surname><given-names>PJ</given-names></name><etal></etal><article-title>Comparative DNA sequence analysis of wheat and rice genomes</article-title><source>Genome Res</source><year>2003</year><volume>13</volume><fpage>1818</fpage><lpage>1827</lpage><pub-id pub-id-type="pmid">12902377</pub-id></mixed-citation></ref><ref id="B12"><mixed-citation publication-type="journal"><name><surname>Francki</surname><given-names>M</given-names></name><name><surname>Carter</surname><given-names>M</given-names></name><name><surname>Ryan</surname><given-names>K</given-names></name><name><surname>Hunter</surname><given-names>A</given-names></name><name><surname>Bellgard</surname><given-names>M</given-names></name><name><surname>Appels</surname><given-names>R</given-names></name><article-title>Comparative organization of wheat homoeologous group 3S and 7L using wheat-rice synteny and identification of potential markers for genes controlling xanthophyll content in wheat</article-title><source>Funct Integr Genomics</source><year>2004</year><volume>4</volume><fpage>118</fpage><lpage>130</lpage><pub-id pub-id-type="doi">10.1007/s10142-004-0110-5</pub-id><pub-id pub-id-type="pmid">15105995</pub-id></mixed-citation></ref><ref id="B13"><mixed-citation publication-type="journal"><name><surname>Todd</surname><given-names>AE</given-names></name><name><surname>Orengo</surname><given-names>CA</given-names></name><name><surname>Thornton</surname><given-names>JM</given-names></name><article-title>Evolution of function in protein superfamilies, from a structural perspective</article-title><source>J Mol Biol</source><year>2001</year><volume>307</volume><fpage>1113</fpage><lpage>1143</lpage><pub-id pub-id-type="doi">10.1006/jmbi.2001.4513</pub-id><pub-id pub-id-type="pmid">11286560</pub-id></mixed-citation></ref><ref id="B14"><mixed-citation publication-type="journal"><collab>International Rice Genome Sequencing Project</collab><article-title>The map-based sequence of the rice genome</article-title><source>Nature</source><year>2005</year><volume>436</volume><fpage>793</fpage><lpage>800</lpage><pub-id pub-id-type="doi">10.1038/nature03895</pub-id><pub-id pub-id-type="pmid">16100779</pub-id></mixed-citation></ref><ref id="B15"><mixed-citation publication-type="journal"><name><surname>Paterson</surname><given-names>AH</given-names></name><name><surname>Bowers</surname><given-names>JE</given-names></name><name><surname>Bruggmann</surname><given-names>R</given-names></name><name><surname>Dubchak</surname><given-names>I</given-names></name><name><surname>Grimwood</surname><given-names>J</given-names></name><name><surname>Gundlach</surname><given-names>H</given-names></name><name><surname>Haberer</surname><given-names>G</given-names></name><name><surname>Hellsten</surname><given-names>U</given-names></name><name><surname>Mitros</surname><given-names>T</given-names></name><name><surname>Poliakov</surname><given-names>A</given-names></name><etal></etal><article-title>The Sorghum bicolor genome and the diversification of grasses</article-title><source>Nature</source><year>2009</year><volume>457</volume><fpage>551</fpage><lpage>556</lpage><pub-id pub-id-type="doi">10.1038/nature07723</pub-id><pub-id pub-id-type="pmid">19189423</pub-id></mixed-citation></ref><ref id="B16"><mixed-citation publication-type="journal"><name><surname>Chantret</surname><given-names>N</given-names></name><name><surname>Cenci</surname><given-names>A</given-names></name><name><surname>Sabot</surname><given-names>F</given-names></name><name><surname>Anderson</surname><given-names>OD</given-names></name><name><surname>Dubcovsky</surname><given-names>J</given-names></name><article-title>Sequencing of the Triticum monococcum hardness locus reveals good microcolinearity with rice</article-title><source>Mol Genet Genomics</source><year>2004</year><volume>271</volume><fpage>377</fpage><lpage>386</lpage><pub-id pub-id-type="doi">10.1007/s00438-004-0991-y</pub-id><pub-id pub-id-type="pmid">15014981</pub-id></mixed-citation></ref><ref id="B17"><mixed-citation publication-type="journal"><name><surname>Faris</surname><given-names>JD</given-names></name><name><surname>Zhang</surname><given-names>Z</given-names></name><name><surname>Fellers</surname><given-names>JP</given-names></name><name><surname>Gill</surname><given-names>BS</given-names></name><article-title>Micro-colinearity between rice, Brachypodium, and Triticum monococcum at the wheat domestication locus Q</article-title><source>Funct Integr Genomics</source><year>2008</year><volume>8</volume><fpage>149</fpage><lpage>164</lpage><pub-id pub-id-type="doi">10.1007/s10142-008-0073-z</pub-id><pub-id pub-id-type="pmid">18210171</pub-id></mixed-citation></ref><ref id="B18"><mixed-citation publication-type="journal"><name><surname>SanMiguel</surname><given-names>P</given-names></name><name><surname>Tikhonov</surname><given-names>A</given-names></name><name><surname>Jin</surname><given-names>YK</given-names></name><name><surname>Motchoulskaia</surname><given-names>N</given-names></name><name><surname>Zakharov</surname><given-names>D</given-names></name><name><surname>Melake-Berhan</surname><given-names>A</given-names></name><name><surname>Springer</surname><given-names>PS</given-names></name><name><surname>Edwards</surname><given-names>KJ</given-names></name><name><surname>Lee</surname><given-names>M</given-names></name><name><surname>Avramova</surname><given-names>Z</given-names></name><etal></etal><article-title>Nested retrotransposons in the intergenic regions of the maize genome</article-title><source>Science</source><year>1996</year><volume>274</volume><fpage>765</fpage><lpage>768</lpage><pub-id pub-id-type="doi">10.1126/science.274.5288.765</pub-id><pub-id pub-id-type="pmid">8864112</pub-id></mixed-citation></ref><ref id="B19"><mixed-citation publication-type="journal"><name><surname>Feuillet</surname><given-names>C</given-names></name><name><surname>Keller</surname><given-names>B</given-names></name><article-title>High gene density is conserved at syntenic loci of small and large grass genomes</article-title><source>Proc Natl Acad Sci USA</source><year>1999</year><volume>96</volume><fpage>8265</fpage><lpage>8270</lpage><pub-id pub-id-type="doi">10.1073/pnas.96.14.8265</pub-id><pub-id pub-id-type="pmid">10393983</pub-id></mixed-citation></ref><ref id="B20"><mixed-citation publication-type="journal"><name><surname>Tikhonov</surname><given-names>AP</given-names></name><name><surname>SanMiguel</surname><given-names>PJ</given-names></name><name><surname>Nakajima</surname><given-names>Y</given-names></name><name><surname>Gorenstein</surname><given-names>NM</given-names></name><name><surname>Bennetzen</surname><given-names>JL</given-names></name><name><surname>Avramova</surname><given-names>Z</given-names></name><article-title>Colinearity and its exceptions in orthologous adh regions of maize and sorghum</article-title><source>Proc Natl Acad Sci USA</source><year>1999</year><volume>96</volume><fpage>7409</fpage><lpage>7414</lpage><pub-id pub-id-type="doi">10.1073/pnas.96.13.7409</pub-id><pub-id pub-id-type="pmid">10377428</pub-id></mixed-citation></ref><ref id="B21"><mixed-citation publication-type="journal"><name><surname>Wicker</surname><given-names>T</given-names></name><name><surname>Stein</surname><given-names>N</given-names></name><name><surname>Albar</surname><given-names>L</given-names></name><name><surname>Feuillet</surname><given-names>C</given-names></name><name><surname>Schlagenhauf</surname><given-names>E</given-names></name><name><surname>Keller</surname><given-names>B</given-names></name><article-title>Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution</article-title><source>Plant J</source><year>2001</year><volume>26</volume><fpage>307</fpage><lpage>316</lpage><pub-id pub-id-type="doi">10.1046/j.1365-313X.2001.01028.x</pub-id><pub-id pub-id-type="pmid">11439119</pub-id></mixed-citation></ref><ref id="B22"><mixed-citation publication-type="journal"><name><surname>Caldwell</surname><given-names>KS</given-names></name><name><surname>Langridge</surname><given-names>P</given-names></name><name><surname>Powell</surname><given-names>W</given-names></name><article-title>Comparative sequence analysis of the region harboring the hardness locus in barley and its colinear region in rice</article-title><source>Plant Physiol</source><year>2004</year><volume>136</volume><fpage>3177</fpage><lpage>3190</lpage><pub-id pub-id-type="doi">10.1104/pp.104.044081</pub-id><pub-id pub-id-type="pmid">15466237</pub-id></mixed-citation></ref><ref id="B23"><mixed-citation publication-type="journal"><name><surname>Ewing</surname><given-names>B</given-names></name><name><surname>Green</surname><given-names>P</given-names></name><article-title>Base-calling of automated sequencer traces using phred. II. Error probabilities</article-title><source>Genome Res</source><year>1998</year><volume>8</volume><fpage>186</fpage><lpage>194</lpage><pub-id pub-id-type="pmid">9521922</pub-id></mixed-citation></ref><ref id="B24"><mixed-citation publication-type="journal"><name><surname>Paux</surname><given-names>E</given-names></name><name><surname>Roger</surname><given-names>D</given-names></name><name><surname>Badaeva</surname><given-names>E</given-names></name><name><surname>Gay</surname><given-names>G</given-names></name><name><surname>Bernard</surname><given-names>M</given-names></name><name><surname>Sourdille</surname><given-names>P</given-names></name><name><surname>Feuillet</surname><given-names>C</given-names></name><article-title>Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B</article-title><source>Plant J</source><year>2006</year><volume>48</volume><fpage>463</fpage><lpage>474</lpage><pub-id pub-id-type="doi">10.1111/j.1365-313X.2006.02891.x</pub-id><pub-id pub-id-type="pmid">17010109</pub-id></mixed-citation></ref><ref id="B25"><mixed-citation publication-type="journal"><name><surname>Bartos</surname><given-names>J</given-names></name><name><surname>Paux</surname><given-names>E</given-names></name><name><surname>Kofler</surname><given-names>R</given-names></name><name><surname>Havrankova</surname><given-names>M</given-names></name><name><surname>Kopecky</surname><given-names>D</given-names></name><name><surname>Suchankova</surname><given-names>P</given-names></name><name><surname>Safar</surname><given-names>J</given-names></name><name><surname>Simkova</surname><given-names>H</given-names></name><name><surname>Town</surname><given-names>CD</given-names></name><name><surname>Lelley</surname><given-names>T</given-names></name><etal></etal><article-title>A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R</article-title><source>BMC Plant Biol</source><year>2008</year><volume>8</volume><fpage>95</fpage><pub-id pub-id-type="doi">10.1186/1471-2229-8-95</pub-id><pub-id pub-id-type="pmid">18803819</pub-id></mixed-citation></ref><ref id="B26"><mixed-citation publication-type="journal"><name><surname>Lehmensiek</surname><given-names>A</given-names></name><name><surname>Eckermann</surname><given-names>PJ</given-names></name><name><surname>Verbyla</surname><given-names>AP</given-names></name><name><surname>Appels</surname><given-names>R</given-names></name><name><surname>Sutherland</surname><given-names>MW</given-names></name><name><surname>Daggard</surname><given-names>GE</given-names></name><article-title>Curation of wheat maps to improve map accuracy and QTL detection</article-title><source>Aus J Agric Res</source><year>2005</year><volume>56</volume><fpage>1347</fpage><lpage>1354</lpage><pub-id pub-id-type="doi">10.1071/AR05126</pub-id></mixed-citation></ref><ref id="B27"><mixed-citation publication-type="journal"><name><surname>Altschul</surname><given-names>SF</given-names></name><name><surname>Gish</surname><given-names>W</given-names></name><name><surname>Miller</surname><given-names>W</given-names></name><name><surname>Myers</surname><given-names>EW</given-names></name><name><surname>Lipman</surname><given-names>DJ</given-names></name><article-title>Basic local alignment search tool</article-title><source>J Mol Biol</source><year>1990</year><volume>215</volume><fpage>403</fpage><lpage>410</lpage><pub-id pub-id-type="pmid">2231712</pub-id></mixed-citation></ref><ref id="B28"><mixed-citation publication-type="journal"><name><surname>Sonnhammer</surname><given-names>EL</given-names></name><name><surname>Durbin</surname><given-names>R</given-names></name><article-title>A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis</article-title><source>Gene</source><year>1995</year><volume>167</volume><fpage>GC1</fpage><lpage>10</lpage><pub-id pub-id-type="doi">10.1016/0378-1119(95)00714-8</pub-id><pub-id pub-id-type="pmid">8566757</pub-id></mixed-citation></ref><ref id="B29"><mixed-citation publication-type="journal"><name><surname>Novikova</surname><given-names>O</given-names></name><article-title>Chromodomains and LTR retrotransposons in plants</article-title><source>Commun Integr Biol</source><year>2009</year><volume>2</volume><fpage>158</fpage><lpage>162</lpage><pub-id pub-id-type="pmid">19513271</pub-id></mixed-citation></ref><ref id="B30"><mixed-citation publication-type="journal"><name><surname>Eddy</surname><given-names>SR</given-names></name><article-title>Profile hidden Markov models</article-title><source>Bioinformatics</source><year>1998</year><volume>14</volume><fpage>755</fpage><lpage>763</lpage><pub-id pub-id-type="doi">10.1093/bioinformatics/14.9.755</pub-id><pub-id pub-id-type="pmid">9918945</pub-id></mixed-citation></ref><ref id="B31"><mixed-citation publication-type="journal"><name><surname>Novikova</surname><given-names>O</given-names></name><name><surname>Mayorov</surname><given-names>V</given-names></name><name><surname>Smyshlyaev</surname><given-names>G</given-names></name><name><surname>Fursov</surname><given-names>M</given-names></name><name><surname>Adkison</surname><given-names>L</given-names></name><name><surname>Pisarenko</surname><given-names>O</given-names></name><name><surname>Blinov</surname><given-names>A</given-names></name><article-title>Novel clades of chromodomain-containing Gypsy LTR retrotransposons from mosses (Bryophyta)</article-title><source>Plant J</source><year>2008</year><volume>56</volume><fpage>562</fpage><lpage>574</lpage><pub-id pub-id-type="doi">10.1111/j.1365-313X.2008.03621.x</pub-id><pub-id pub-id-type="pmid">18643967</pub-id></mixed-citation></ref><ref id="B32"><mixed-citation publication-type="journal"><name><surname>Paro</surname><given-names>R</given-names></name><name><surname>Hogness</surname><given-names>DS</given-names></name><article-title>The Polycomb protein shares a homologous domain with a heterochromatin-associated protein of Drosophila</article-title><source>Proc Natl Acad Sci USA</source><year>1991</year><volume>88</volume><fpage>263</fpage><lpage>267</lpage><pub-id pub-id-type="doi">10.1073/pnas.88.1.263</pub-id><pub-id pub-id-type="pmid">1898775</pub-id></mixed-citation></ref><ref id="B33"><mixed-citation publication-type="journal"><name><surname>Elgin</surname><given-names>SC</given-names></name><article-title>Heterochromatin and gene regulation in Drosophila</article-title><source>Curr Opin Genet Dev</source><year>1996</year><volume>6</volume><fpage>193</fpage><lpage>202</lpage><pub-id pub-id-type="doi">10.1016/S0959-437X(96)80050-5</pub-id><pub-id pub-id-type="pmid">8722176</pub-id></mixed-citation></ref><ref id="B34"><mixed-citation publication-type="journal"><name><surname>Lloréns</surname><given-names>C</given-names></name><name><surname>Futami</surname><given-names>R</given-names></name><name><surname>Bezemer</surname><given-names>D</given-names></name><name><surname>Moya</surname><given-names>A</given-names></name><article-title>The Gypsy Database (GyDB) of mobile genetic elements</article-title><source>Nucleic Acids Res</source><year>2008</year><volume>36</volume><fpage>D38</fpage><lpage>46</lpage><pub-id pub-id-type="doi">10.1093/nar/gkm697</pub-id><pub-id pub-id-type="pmid">17895280</pub-id></mixed-citation></ref><ref id="B35"><mixed-citation publication-type="journal"><name><surname>Nagaki</surname><given-names>K</given-names></name><name><surname>Tsujimoto</surname><given-names>H</given-names></name><name><surname>Isono</surname><given-names>K</given-names></name><name><surname>Sasakuma</surname><given-names>T</given-names></name><article-title>Molecular characterization of a tandem repeat, Afa family, and its distribution among Triticeae</article-title><source>Genome</source><year>1995</year><volume>38</volume><fpage>479</fpage><lpage>486</lpage><pub-id pub-id-type="pmid">7557360</pub-id></mixed-citation></ref><ref id="B36"><mixed-citation publication-type="journal"><name><surname>Zhang</surname><given-names>Q</given-names></name><name><surname>Arbuckle</surname><given-names>J</given-names></name><name><surname>Wessler</surname><given-names>SR</given-names></name><article-title>Recent, extensive, and preferential insertion of members of the miniature inverted-repeat transposable element family Heartbreaker into genic regions of maize</article-title><source>Proc Natl Acad Sci USA</source><year>2000</year><volume>97</volume><fpage>1160</fpage><lpage>1165</lpage><pub-id pub-id-type="doi">10.1073/pnas.97.3.1160</pub-id><pub-id pub-id-type="pmid">10655501</pub-id></mixed-citation></ref><ref id="B37"><mixed-citation publication-type="journal"><name><surname>Majoros</surname><given-names>WH</given-names></name><name><surname>Pertea</surname><given-names>M</given-names></name><name><surname>Salzberg</surname><given-names>SL</given-names></name><article-title>TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders</article-title><source>Bioinformatics</source><year>2004</year><volume>20</volume><fpage>2878</fpage><lpage>2879</lpage><pub-id pub-id-type="doi">10.1093/bioinformatics/bth315</pub-id><pub-id pub-id-type="pmid">15145805</pub-id></mixed-citation></ref><ref id="B38"><mixed-citation publication-type="journal"><name><surname>Ouyang</surname><given-names>S</given-names></name><name><surname>Zhu</surname><given-names>W</given-names></name><name><surname>Hamilton</surname><given-names>J</given-names></name><name><surname>Lin</surname><given-names>H</given-names></name><name><surname>Campbell</surname><given-names>M</given-names></name><name><surname>Childs</surname><given-names>K</given-names></name><name><surname>Thibaud-Nissen</surname><given-names>F</given-names></name><name><surname>Malek</surname><given-names>RL</given-names></name><name><surname>Lee</surname><given-names>Y</given-names></name><name><surname>Zheng</surname><given-names>L</given-names></name><etal></etal><article-title>The TIGR Rice Genome Annotation Resource: improvements and new features</article-title><source>Nucleic Acids Res</source><year>2007</year><volume>35</volume><fpage>D883</fpage><lpage>887</lpage><pub-id pub-id-type="doi">10.1093/nar/gkl976</pub-id><pub-id pub-id-type="pmid">17145706</pub-id></mixed-citation></ref><ref id="B39"><mixed-citation publication-type="journal"><name><surname>Kikuchi</surname><given-names>S</given-names></name><name><surname>Satoh</surname><given-names>K</given-names></name><name><surname>Nagata</surname><given-names>T</given-names></name><name><surname>Kawagashira</surname><given-names>N</given-names></name><name><surname>Doi</surname><given-names>K</given-names></name><name><surname>Kishimoto</surname><given-names>N</given-names></name><name><surname>Yazaki</surname><given-names>J</given-names></name><name><surname>Ishikawa</surname><given-names>M</given-names></name><collab>Rice Full-Length cDNA Consortium, National Institute of Agrobiological Sciences Rice Full-Length cDNA Project Team</collab><etal></etal><article-title>Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice</article-title><source>Science</source><year>2003</year><volume>301</volume><fpage>376</fpage><lpage>379</lpage><pub-id pub-id-type="doi">10.1126/science.1081288</pub-id><pub-id pub-id-type="pmid">12869764</pub-id></mixed-citation></ref><ref id="B40"><mixed-citation publication-type="journal"><name><surname>Silverstein</surname><given-names>KA</given-names></name><name><surname>Moskal</surname><given-names>WA</given-names></name><name><surname>Wu</surname><given-names>HC</given-names></name><name><surname>Underwood</surname><given-names>BA</given-names></name><name><surname>Graham</surname><given-names>MA</given-names></name><name><surname>Town</surname><given-names>CD</given-names></name><name><surname>VandenBosch</surname><given-names>KA</given-names></name><article-title>Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants</article-title><source>Plant J</source><year>2007</year><volume>51</volume><fpage>262</fpage><lpage>280</lpage><pub-id pub-id-type="doi">10.1111/j.1365-313X.2007.03136.x</pub-id><pub-id pub-id-type="pmid">17565583</pub-id></mixed-citation></ref><ref id="B41"><mixed-citation publication-type="journal"><name><surname>Graham</surname><given-names>MA</given-names></name><name><surname>Silverstein</surname><given-names>KA</given-names></name><name><surname>Cannon</surname><given-names>SB</given-names></name><name><surname>VandenBosch</surname><given-names>KA</given-names></name><article-title>Computational identification and characterization of novel genes from legumes</article-title><source>Plant Physiol</source><year>2004</year><volume>135</volume><fpage>1179</fpage><lpage>1197</lpage><pub-id pub-id-type="doi">10.1104/pp.104.037531</pub-id><pub-id pub-id-type="pmid">15266052</pub-id></mixed-citation></ref><ref id="B42"><mixed-citation publication-type="journal"><name><surname>Ouyang</surname><given-names>S</given-names></name><name><surname>Buell</surname><given-names>CR</given-names></name><article-title>The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants</article-title><source>Nucleic Acids Res</source><year>2004</year><volume>32</volume><fpage>D360</fpage><lpage>363</lpage><pub-id pub-id-type="doi">10.1093/nar/gkh099</pub-id><pub-id pub-id-type="pmid">14681434</pub-id></mixed-citation></ref><ref id="B43"><mixed-citation publication-type="journal"><collab>Arabidopsis Genome Initiative</collab><article-title>Analysis of the genome sequence of the flowering plant Arabidopsis thaliana</article-title><source>Nature</source><year>2000</year><volume>408</volume><fpage>796</fpage><lpage>815</lpage><pub-id pub-id-type="doi">10.1038/35048692</pub-id><pub-id pub-id-type="pmid">11130711</pub-id></mixed-citation></ref><ref id="B44"><mixed-citation publication-type="journal"><name><surname>Jaillon</surname><given-names>O</given-names></name><name><surname>Aury</surname><given-names>JM</given-names></name><name><surname>Noel</surname><given-names>B</given-names></name><name><surname>Policriti</surname><given-names>A</given-names></name><name><surname>Clepet</surname><given-names>C</given-names></name><name><surname>Casagrande</surname><given-names>A</given-names></name><name><surname>Choisne</surname><given-names>N</given-names></name><name><surname>Aubourg</surname><given-names>S</given-names></name><name><surname>Vitulo</surname><given-names>N</given-names></name><name><surname>Jubin</surname><given-names>C</given-names></name><etal></etal><article-title>The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla</article-title><source>Nature</source><year>2007</year><volume>449</volume><fpage>463</fpage><lpage>467</lpage><pub-id pub-id-type="doi">10.1038/nature06148</pub-id><pub-id pub-id-type="pmid">17721507</pub-id></mixed-citation></ref><ref id="B45"><mixed-citation publication-type="journal"><name><surname>Tatusova</surname><given-names>TA</given-names></name><name><surname>Madden</surname><given-names>TL</given-names></name><article-title>BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences</article-title><source>FEMS Microbiol Lett</source><year>1999</year><volume>174</volume><fpage>247</fpage><lpage>250</lpage><pub-id pub-id-type="doi">10.1111/j.1574-6968.1999.tb13575.x</pub-id><pub-id pub-id-type="pmid">10339815</pub-id></mixed-citation></ref><ref id="B46"><mixed-citation publication-type="journal"><name><surname>Chantret</surname><given-names>N</given-names></name><name><surname>Salse</surname><given-names>J</given-names></name><name><surname>Sabot</surname><given-names>F</given-names></name><name><surname>Bellec</surname><given-names>A</given-names></name><name><surname>Laubin</surname><given-names>B</given-names></name><name><surname>Dubois</surname><given-names>I</given-names></name><name><surname>Dossat</surname><given-names>C</given-names></name><name><surname>Sourdille</surname><given-names>P</given-names></name><name><surname>Joudrier</surname><given-names>P</given-names></name><name><surname>Gautier</surname><given-names>MF</given-names></name><etal></etal><article-title>Contrasted microcolinearity and gene evolution within a homoeologous region of wheat and barley species</article-title><source>J Mol Evol</source><year>2008</year><volume>66</volume><fpage>138</fpage><lpage>150</lpage><pub-id pub-id-type="doi">10.1007/s00239-008-9066-8</pub-id><pub-id pub-id-type="pmid">18274696</pub-id></mixed-citation></ref><ref id="B47"><mixed-citation publication-type="journal"><name><surname>Brooks</surname><given-names>SA</given-names></name><name><surname>Huang</surname><given-names>L</given-names></name><name><surname>Herbel</surname><given-names>MN</given-names></name><name><surname>Gill</surname><given-names>BS</given-names></name><name><surname>Brown-Guedira</surname><given-names>G</given-names></name><name><surname>Fellers</surname><given-names>JP</given-names></name><article-title>Structural variation and evolution of a defense-gene cluster in natural populations of Aegilops tauschii</article-title><source>Theor Appl Genet</source><year>2006</year><volume>112</volume><fpage>618</fpage><lpage>626</lpage><pub-id pub-id-type="doi">10.1007/s00122-005-0160-7</pub-id><pub-id pub-id-type="pmid">16402192</pub-id></mixed-citation></ref><ref id="B48"><mixed-citation publication-type="journal"><name><surname>Bennetzen</surname><given-names>JL</given-names></name><name><surname>Ramakrishna</surname><given-names>W</given-names></name><article-title>Numerous small rearrangements of gene content, order and orientation differentiate grass genomes</article-title><source>Plant Mol Biol</source><year>2002</year><volume>48</volume><issue>5-6</issue><fpage>821</fpage><lpage>7</lpage><pub-id pub-id-type="doi">10.1023/A:1014841515249</pub-id><pub-id pub-id-type="pmid">11999852</pub-id></mixed-citation></ref><ref id="B49"><mixed-citation publication-type="journal"><name><surname>Guyot</surname><given-names>R</given-names></name><name><surname>Yahiaoui</surname><given-names>N</given-names></name><name><surname>Feuillet</surname><given-names>C</given-names></name><name><surname>Keller</surname><given-names>B</given-names></name><article-title>In silico comparative analysis reveals a mosaic conservation of genes within a novel colinear region in wheat chromosome 1AS and rice chromosome 5S</article-title><source>Funct Integr Genomics</source><year>2004</year><volume>4</volume><issue>1</issue><fpage>47</fpage><lpage>58</lpage><pub-id pub-id-type="doi">10.1007/s10142-004-0103-4</pub-id><pub-id pub-id-type="pmid">14767678</pub-id></mixed-citation></ref><ref id="B50"><mixed-citation publication-type="journal"><name><surname>Mefford</surname><given-names>H</given-names></name><name><surname>Sharp</surname><given-names>A</given-names></name><name><surname>Baker</surname><given-names>C</given-names></name><name><surname>Itsara</surname><given-names>A</given-names></name><name><surname>Jiang</surname><given-names>Z</given-names></name><name><surname>Buysse</surname><given-names>K</given-names></name><name><surname>Huang</surname><given-names>S</given-names></name><name><surname>Maloney</surname><given-names>V</given-names></name><name><surname>Crolla</surname><given-names>J</given-names></name><name><surname>Baralle</surname><given-names>D</given-names></name><name><surname>Collins</surname><given-names>A</given-names></name><etal></etal><article-title>Recurrent Rearrangements of Chromosome 1q21.1 and Variable Pediatric Phenotypes</article-title><source>N Engl J Med</source><year>2008</year><volume>359</volume><issue>16</issue><fpage>1685</fpage><lpage>99</lpage><pub-id pub-id-type="doi">10.1056/NEJMoa0805384</pub-id><pub-id pub-id-type="pmid">18784092</pub-id></mixed-citation></ref><ref id="B51"><mixed-citation publication-type="journal"><name><surname>Kellogg</surname><given-names>EA</given-names></name><article-title>Evolutionary history of the grasses</article-title><source>Plant Physiol</source><year>2001</year><volume>125</volume><fpage>1198</fpage><lpage>1205</lpage><pub-id pub-id-type="doi">10.1104/pp.125.3.1198</pub-id><pub-id pub-id-type="pmid">11244101</pub-id></mixed-citation></ref><ref id="B52"><mixed-citation publication-type="journal"><name><surname>Lai</surname><given-names>J</given-names></name><name><surname>Li</surname><given-names>Y</given-names></name><name><surname>Messing</surname><given-names>J</given-names></name><name><surname>Dooner</surname><given-names>HK</given-names></name><article-title>Gene movement by Helitron transposons contributes to the haplotype variability of maize</article-title><source>Proc Natl Acad Sci USA</source><year>2005</year><volume>102</volume><fpage>9068</fpage><lpage>9073</lpage><pub-id pub-id-type="doi">10.1073/pnas.0502923102</pub-id><pub-id pub-id-type="pmid">15951422</pub-id></mixed-citation></ref><ref id="B53"><mixed-citation publication-type="journal"><name><surname>Lal</surname><given-names>SK</given-names></name><name><surname>Hannah</surname><given-names>LC</given-names></name><article-title>Plant genomes: massive changes of the maize genome are caused by Helitrons</article-title><source>Heredity</source><year>2005</year><volume>95</volume><fpage>421</fpage><lpage>422</lpage><pub-id pub-id-type="doi">10.1038/sj.hdy.6800764</pub-id><pub-id pub-id-type="pmid">16222326</pub-id></mixed-citation></ref><ref id="B54"><mixed-citation publication-type="journal"><name><surname>Buckler</surname><given-names>ES</given-names></name><name><surname>Gaut</surname><given-names>BS</given-names></name><name><surname>McMullen</surname><given-names>MD</given-names></name><article-title>Molecular and functional diversity of maize</article-title><source>Curr Opin Plant Biol</source><year>2006</year><volume>9</volume><fpage>172</fpage><lpage>176</lpage><pub-id pub-id-type="doi">10.1016/j.pbi.2006.01.013</pub-id><pub-id pub-id-type="pmid">16459128</pub-id></mixed-citation></ref><ref id="B55"><mixed-citation publication-type="journal"><name><surname>Wicker</surname><given-names>T</given-names></name><name><surname>Guyot</surname><given-names>R</given-names></name><name><surname>Yahiaoui</surname><given-names>N</given-names></name><name><surname>Keller</surname><given-names>B</given-names></name><article-title>CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements</article-title><source>Plant Physiol</source><year>2003</year><volume>132</volume><fpage>52</fpage><lpage>63</lpage><pub-id pub-id-type="doi">10.1104/pp.102.015743</pub-id><pub-id pub-id-type="pmid">12746511</pub-id></mixed-citation></ref><ref id="B56"><mixed-citation publication-type="journal"><name><surname>Sabot</surname><given-names>F</given-names></name><name><surname>Guyot</surname><given-names>R</given-names></name><name><surname>Wicker</surname><given-names>T</given-names></name><name><surname>Chantret</surname><given-names>N</given-names></name><name><surname>Laubin</surname><given-names>B</given-names></name><name><surname>Chalhoub</surname><given-names>B</given-names></name><name><surname>Leroy</surname><given-names>P</given-names></name><name><surname>Sourdille</surname><given-names>P</given-names></name><name><surname>Bernard</surname><given-names>M</given-names></name><article-title>Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations</article-title><source>Mol Genet Genomics</source><year>2005</year><volume>274</volume><fpage>119</fpage><lpage>130</lpage><pub-id pub-id-type="doi">10.1007/s00438-005-0012-9</pub-id><pub-id pub-id-type="pmid">16034625</pub-id></mixed-citation></ref><ref id="B57"><mixed-citation publication-type="journal"><name><surname>Jiang</surname><given-names>N</given-names></name><name><surname>Bao</surname><given-names>Z</given-names></name><name><surname>Zhang</surname><given-names>X</given-names></name><name><surname>Eddy</surname><given-names>SR</given-names></name><name><surname>Wessler</surname><given-names>SR</given-names></name><article-title>Pack-MULE transposable elements mediate gene evolution in plants</article-title><source>Nature</source><year>2004</year><volume>431</volume><fpage>569</fpage><lpage>573</lpage><pub-id pub-id-type="doi">10.1038/nature02953</pub-id><pub-id pub-id-type="pmid">15457261</pub-id></mixed-citation></ref><ref id="B58"><mixed-citation publication-type="journal"><name><surname>Brooks</surname><given-names>SA</given-names></name><name><surname>Huang</surname><given-names>L</given-names></name><name><surname>Gill</surname><given-names>BS</given-names></name><name><surname>Fellers</surname><given-names>JP</given-names></name><article-title>Analysis of 106 kb of contiguous DNA sequence from the D genome of wheat reveals high gene density and a complex arrangement of genes related to disease resistance</article-title><source>Genome</source><year>2002</year><volume>45</volume><fpage>963</fpage><lpage>972</lpage><pub-id pub-id-type="doi">10.1139/g02-049</pub-id><pub-id pub-id-type="pmid">12416630</pub-id></mixed-citation></ref><ref id="B59"><mixed-citation publication-type="journal"><name><surname>Qi</surname><given-names>L</given-names></name><name><surname>Echalier</surname><given-names>B</given-names></name><name><surname>Friebe</surname><given-names>B</given-names></name><name><surname>Gill</surname><given-names>BS</given-names></name><article-title>Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs</article-title><source>Funct Integr Genomics</source><year>2003</year><volume>3</volume><fpage>39</fpage><lpage>55</lpage><pub-id pub-id-type="pmid">12590342</pub-id></mixed-citation></ref><ref id="B60"><mixed-citation publication-type="journal"><name><surname>Gill</surname><given-names>KS</given-names></name><name><surname>Gill</surname><given-names>BS</given-names></name><name><surname>Endo</surname><given-names>TR</given-names></name><name><surname>Taylor</surname><given-names>T</given-names></name><article-title>Identification and high-density mapping of gene-rich regions in chromosome group 1 of wheat</article-title><source>Genetics</source><year>1996</year><volume>144</volume><fpage>1883</fpage><lpage>1891</lpage><pub-id pub-id-type="pmid">8978071</pub-id></mixed-citation></ref><ref id="B61"><mixed-citation publication-type="journal"><name><surname>Faris</surname><given-names>JD</given-names></name><name><surname>Haen</surname><given-names>KM</given-names></name><name><surname>Gill</surname><given-names>BS</given-names></name><article-title>Saturation mapping of a gene-rich recombination hot spot region in wheat</article-title><source>Genetics</source><year>2000</year><volume>154</volume><fpage>823</fpage><lpage>835</lpage><pub-id pub-id-type="pmid">10655233</pub-id></mixed-citation></ref><ref id="B62"><mixed-citation publication-type="journal"><name><surname>Komatsuda</surname><given-names>T</given-names></name><name><surname>Pourkheirandish</surname><given-names>M</given-names></name><name><surname>He</surname><given-names>C</given-names></name><name><surname>Azhaguvel</surname><given-names>P</given-names></name><name><surname>Kanamori</surname><given-names>H</given-names></name><name><surname>Perovic</surname><given-names>D</given-names></name><name><surname>Stein</surname><given-names>N</given-names></name><name><surname>Graner</surname><given-names>A</given-names></name><name><surname>Wicker</surname><given-names>T</given-names></name><name><surname>Tagiri</surname><given-names>A</given-names></name><etal></etal><article-title>Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene</article-title><source>Proc Natl Acad Sci USA</source><year>2007</year><volume>104</volume><fpage>1424</fpage><lpage>1429</lpage><pub-id pub-id-type="doi">10.1073/pnas.0608580104</pub-id><pub-id pub-id-type="pmid">17220272</pub-id></mixed-citation></ref><ref id="B63"><mixed-citation publication-type="journal"><name><surname>Dvorak</surname><given-names>J</given-names></name><name><surname>Akhunov</surname><given-names>ED</given-names></name><name><surname>Akhunov</surname><given-names>AR</given-names></name><name><surname>Deal</surname><given-names>KR</given-names></name><name><surname>Luo</surname><given-names>MC</given-names></name><article-title>Molecular characterization of a diagnostic DNA marker for domesticated tetraploid wheat provides evidence for gene flow from wild tetraploid wheat to hexaploid wheat</article-title><source>Mol Biol Evol</source><year>2006</year><volume>23</volume><fpage>1386</fpage><lpage>1396</lpage><pub-id pub-id-type="doi">10.1093/molbev/msl004</pub-id><pub-id pub-id-type="pmid">16675504</pub-id></mixed-citation></ref><ref id="B64"><mixed-citation publication-type="journal"><name><surname>SanMiguel</surname><given-names>PJ</given-names></name><name><surname>Ramakrishna</surname><given-names>W</given-names></name><name><surname>Bennetzen</surname><given-names>JL</given-names></name><name><surname>Busso</surname><given-names>CS</given-names></name><name><surname>Dubcovsky</surname><given-names>J</given-names></name><article-title>Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5A(m)</article-title><source>Funct Integr Genomics</source><year>2002</year><volume>2</volume><fpage>70</fpage><lpage>80</lpage><pub-id pub-id-type="doi">10.1007/s10142-002-0056-4</pub-id><pub-id pub-id-type="pmid">12021852</pub-id></mixed-citation></ref><ref id="B65"><mixed-citation publication-type="journal"><name><surname>Gao</surname><given-names>X</given-names></name><name><surname>Hou</surname><given-names>Y</given-names></name><name><surname>Ebina</surname><given-names>H</given-names></name><name><surname>Levin</surname><given-names>HL</given-names></name><name><surname>Voytas</surname><given-names>DF</given-names></name><article-title>Chromodomains direct integration of retrotransposons to heterochromatin</article-title><source>Genome Res</source><year>2008</year><volume>18</volume><fpage>359</fpage><lpage>369</lpage><pub-id pub-id-type="doi">10.1101/gr.7146408</pub-id><pub-id pub-id-type="pmid">18256242</pub-id></mixed-citation></ref><ref id="B66"><mixed-citation publication-type="journal"><name><surname>Künzel</surname><given-names>G</given-names></name><name><surname>Korzun</surname><given-names>L</given-names></name><name><surname>Meister</surname><given-names>A</given-names></name><article-title>Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints</article-title><source>Genetics</source><year>2000</year><volume>154</volume><fpage>397</fpage><lpage>412</lpage><pub-id pub-id-type="pmid">10628998</pub-id></mixed-citation></ref><ref id="B67"><mixed-citation publication-type="journal"><name><surname>Chandler</surname><given-names>VL</given-names></name><name><surname>Alleman</surname><given-names>M</given-names></name><article-title>Paramutation: Epigenetic Instructions Passed Across Generations</article-title><source>Genetics</source><year>2008</year><volume>178</volume><issue>4</issue><fpage>1839</fpage><lpage>4</lpage><pub-id pub-id-type="pmid">18430919</pub-id></mixed-citation></ref><ref id="B68"><mixed-citation publication-type="journal"><name><surname>Volpe</surname><given-names>T</given-names></name><name><surname>Schramke</surname><given-names>V</given-names></name><name><surname>Hamilton</surname><given-names>GL</given-names></name><name><surname>White</surname><given-names>S</given-names></name><name><surname>Teng</surname><given-names>G</given-names></name><name><surname>Martienssen</surname><given-names>RA</given-names></name><name><surname>Allshire</surname><given-names>RC</given-names></name><article-title>RNA interference is required for normal centromere function in fission yeast</article-title><source>Chromosome Res</source><year>2003</year><volume>11</volume><fpage>137</fpage><lpage>146</lpage><pub-id pub-id-type="doi">10.1023/A:1022815931524</pub-id><pub-id pub-id-type="pmid">12733640</pub-id></mixed-citation></ref><ref id="B69"><mixed-citation publication-type="journal"><name><surname>May</surname><given-names>BP</given-names></name><name><surname>Lippman</surname><given-names>ZB</given-names></name><name><surname>Fang</surname><given-names>Y</given-names></name><name><surname>Spector</surname><given-names>DL</given-names></name><name><surname>Martienssen</surname><given-names>RA</given-names></name><article-title>Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats</article-title><source>PLoS Genet</source><year>2005</year><volume>1</volume><fpage>e79</fpage><pub-id pub-id-type="doi">10.1371/journal.pgen.0010079</pub-id><pub-id pub-id-type="pmid">16389298</pub-id></mixed-citation></ref><ref id="B70"><mixed-citation publication-type="journal"><name><surname>Vagin</surname><given-names>VV</given-names></name><name><surname>Sigova</surname><given-names>A</given-names></name><name><surname>Li</surname><given-names>C</given-names></name><name><surname>Seitz</surname><given-names>H</given-names></name><name><surname>Gvozdev</surname><given-names>V</given-names></name><name><surname>Zamore</surname><given-names>PD</given-names></name><article-title>A distinct small RNA pathway silences selfish genetic elements in the germline</article-title><source>Science</source><year>2006</year><volume>313</volume><fpage>320</fpage><lpage>324</lpage><pub-id pub-id-type="doi">10.1126/science.1129333</pub-id><pub-id pub-id-type="pmid">16809489</pub-id></mixed-citation></ref><ref id="B71"><mixed-citation publication-type="journal"><name><surname>Kim</surname><given-names>M</given-names></name><name><surname>Vasiljeva</surname><given-names>L</given-names></name><name><surname>Rando</surname><given-names>OJ</given-names></name><name><surname>Zhelkovsky</surname><given-names>A</given-names></name><name><surname>Moore</surname><given-names>C</given-names></name><name><surname>Buratowski</surname><given-names>S</given-names></name><article-title>Distinct pathways for snoRNA and mRNA termination</article-title><source>Mol Cell</source><year>2006</year><volume>24</volume><fpage>723</fpage><lpage>734</lpage><pub-id pub-id-type="doi">10.1016/j.molcel.2006.11.011</pub-id><pub-id pub-id-type="pmid">17157255</pub-id></mixed-citation></ref><ref id="B72"><mixed-citation publication-type="journal"><name><surname>Sourdille</surname><given-names>P</given-names></name><name><surname>Singh</surname><given-names>S</given-names></name><name><surname>Cadalen</surname><given-names>T</given-names></name><name><surname>Brown-Guedira</surname><given-names>GL</given-names></name><name><surname>Gay</surname><given-names>G</given-names></name><name><surname>Qi</surname><given-names>L</given-names></name><name><surname>Gill</surname><given-names>BS</given-names></name><name><surname>Dufour</surname><given-names>P</given-names></name><name><surname>Murigneux</surname><given-names>A</given-names></name><name><surname>Bernard</surname><given-names>M</given-names></name><article-title>Microsatellite-based deletion bin system for the establishment of genetic-physical map relationships in wheat (Triticum aestivum L.)</article-title><source>Funct Integr Genomics</source><year>2004</year><volume>4</volume><fpage>12</fpage><lpage>25</lpage><pub-id pub-id-type="doi">10.1007/s10142-004-0106-1</pub-id><pub-id pub-id-type="pmid">15004738</pub-id></mixed-citation></ref><ref id="B73"><mixed-citation publication-type="journal"><name><surname>Burge</surname><given-names>C</given-names></name><name><surname>Karlin</surname><given-names>S</given-names></name><article-title>Prediction of complete gene structures in human genomic DNA</article-title><source>J Mol Biol</source><year>1997</year><volume>268</volume><issue>1</issue><fpage>78</fpage><lpage>94</lpage><pub-id pub-id-type="doi">10.1006/jmbi.1997.0951</pub-id><pub-id pub-id-type="pmid">9149143</pub-id></mixed-citation></ref><ref id="B74"><mixed-citation publication-type="journal"><name><surname>Finn</surname><given-names>RD</given-names></name><name><surname>Tate</surname><given-names>J</given-names></name><name><surname>Mistry</surname><given-names>J</given-names></name><name><surname>Coggill</surname><given-names>PC</given-names></name><name><surname>Sammut</surname><given-names>SJ</given-names></name><name><surname>Hotz</surname><given-names>HR</given-names></name><name><surname>Ceric</surname><given-names>G</given-names></name><name><surname>Forslund</surname><given-names>K</given-names></name><name><surname>Eddy</surname><given-names>SR</given-names></name><name><surname>Sonnhammer</surname><given-names>EL</given-names></name><etal></etal><article-title>The Pfam protein families database</article-title><source>Nucleic Acids Res</source><year>2008</year><volume>36</volume><fpage>D281</fpage><lpage>288</lpage><pub-id pub-id-type="doi">10.1093/nar/gkm960</pub-id><pub-id pub-id-type="pmid">18039703</pub-id></mixed-citation></ref><ref id="B75"><mixed-citation publication-type="journal"><name><surname>Marchler-Bauer</surname><given-names>A</given-names></name><name><surname>Anderson</surname><given-names>JB</given-names></name><name><surname>Derbyshire</surname><given-names>MK</given-names></name><name><surname>DeWeese-Scott</surname><given-names>C</given-names></name><name><surname>Gonzales</surname><given-names>NR</given-names></name><name><surname>Gwadz</surname><given-names>M</given-names></name><name><surname>Hao</surname><given-names>L</given-names></name><name><surname>He</surname><given-names>S</given-names></name><name><surname>Hurwitz</surname><given-names>DI</given-names></name><name><surname>Jackson</surname><given-names>JD</given-names></name><etal></etal><article-title>CDD: a conserved domain database for interactive domain family analysis</article-title><source>Nucleic Acids Res</source><year>2007</year><volume>35</volume><fpage>D237</fpage><lpage>240</lpage><pub-id pub-id-type="doi">10.1093/nar/gkl951</pub-id><pub-id pub-id-type="pmid">17135202</pub-id></mixed-citation></ref><ref id="B76"><mixed-citation publication-type="journal"><name><surname>Quevillon</surname><given-names>E</given-names></name><name><surname>Silventoinen</surname><given-names>V</given-names></name><name><surname>Pillai</surname><given-names>S</given-names></name><name><surname>Harte</surname><given-names>N</given-names></name><name><surname>Mulder</surname><given-names>N</given-names></name><name><surname>Apweiler</surname><given-names>R</given-names></name><name><surname>Lopez</surname><given-names>R</given-names></name><article-title>InterProScan: protein domains identifier</article-title><source>Nucleic Acids Res</source><year>2005</year><volume>33</volume><fpage>W116</fpage><lpage>120</lpage><pub-id pub-id-type="doi">10.1093/nar/gki442</pub-id><pub-id pub-id-type="pmid">15980438</pub-id></mixed-citation></ref><ref id="B77"><mixed-citation publication-type="journal"><name><surname>Apweiler</surname><given-names>R</given-names></name><name><surname>Attwood</surname><given-names>TK</given-names></name><name><surname>Bairoch</surname><given-names>A</given-names></name><name><surname>Bateman</surname><given-names>A</given-names></name><name><surname>Birney</surname><given-names>E</given-names></name><name><surname>Biswas</surname><given-names>M</given-names></name><name><surname>Bucher</surname><given-names>P</given-names></name><name><surname>Cerutti</surname><given-names>L</given-names></name><name><surname>Corpet</surname><given-names>F</given-names></name><name><surname>Croning</surname><given-names>MD</given-names></name><etal></etal><article-title>The InterPro database, an integrated documentation resource for protein families, domains and functional sites</article-title><source>Nucleic Acids Res</source><year>2001</year><volume>29</volume><fpage>37</fpage><lpage>40</lpage><pub-id pub-id-type="doi">10.1093/nar/29.1.37</pub-id><pub-id pub-id-type="pmid">11125043</pub-id></mixed-citation></ref><ref id="B78"><mixed-citation publication-type="journal"><name><surname>Thompson</surname><given-names>JD</given-names></name><name><surname>Gibson</surname><given-names>TJ</given-names></name><name><surname>Higgins</surname><given-names>DG</given-names></name><article-title>Multiple sequence alignment using ClustalW and ClustalX</article-title><source>Current protocols in bioinformatics/editoral board, Andreas D Baxevanis [et al]</source><year>2002</year><volume>Chapter 2</volume><issue>Unit 2.3</issue><pub-id pub-id-type="pmid">18792934</pub-id></mixed-citation></ref><ref id="B79"><mixed-citation publication-type="journal"><name><surname>Schwartz</surname><given-names>S</given-names></name><name><surname>Elnitski</surname><given-names>L</given-names></name><name><surname>Li</surname><given-names>M</given-names></name><name><surname>Weirauch</surname><given-names>M</given-names></name><name><surname>Riemer</surname><given-names>C</given-names></name><name><surname>Smit</surname><given-names>A</given-names></name><name><surname>Program</surname><given-names>NCS</given-names></name><name><surname>Green</surname><given-names>ED</given-names></name><name><surname>Hardison</surname><given-names>RC</given-names></name><name><surname>Miller</surname><given-names>W</given-names></name><article-title>MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences</article-title><source>Nucleic Acids Res</source><year>2003</year><volume>31</volume><fpage>3518</fpage><lpage>3524</lpage><pub-id pub-id-type="doi">10.1093/nar/gkg579</pub-id><pub-id pub-id-type="pmid">12824357</pub-id></mixed-citation></ref><ref id="B80"><mixed-citation publication-type="other"><name><surname>Nozaki</surname><given-names>Y</given-names></name><name><surname>Macgregor</surname><given-names>A</given-names></name><name><surname>Smith</surname><given-names>C</given-names></name><name><surname>Hunter</surname><given-names>A</given-names></name><name><surname>Bellgard</surname><given-names>M</given-names></name><article-title>Multidotter: Dot-Matrix Program for Multiple Sequences</article-title><source>The 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'05), Las Vegas, USA</source><year>2005</year></mixed-citation></ref><ref id="B81"><mixed-citation publication-type="journal"><name><surname>Darling</surname><given-names>AC</given-names></name><name><surname>Mau</surname><given-names>B</given-names></name><name><surname>Blattner</surname><given-names>FR</given-names></name><name><surname>Perna</surname><given-names>NT</given-names></name><article-title>Mauve: multiple alignment of conserved genomic sequence with rearrangements</article-title><source>Genome Res</source><year>2004</year><volume>14</volume><fpage>1394</fpage><lpage>1403</lpage><pub-id pub-id-type="doi">10.1101/gr.2289704</pub-id><pub-id pub-id-type="pmid">15231754</pub-id></mixed-citation></ref><ref id="B82"><mixed-citation publication-type="journal"><name><surname>Carver</surname><given-names>TJ</given-names></name><name><surname>Rutherford</surname><given-names>KM</given-names></name><name><surname>Berriman</surname><given-names>M</given-names></name><name><surname>Rajandream</surname><given-names>MA</given-names></name><name><surname>Barrell</surname><given-names>BG</given-names></name><name><surname>Parkhill</surname><given-names>J</given-names></name><article-title>ACT: the Artemis Comparison Tool</article-title><source>Bioinformatics</source><year>2005</year><volume>21</volume><fpage>3422</fpage><lpage>3423</lpage><pub-id pub-id-type="doi">10.1093/bioinformatics/bti553</pub-id><pub-id pub-id-type="pmid">15976072</pub-id></mixed-citation></ref></ref-list></back></pmc></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Asie/explor/AustralieFrV1/Data/Pmc/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002300 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Corpus/biblio.hfd -nk 002300 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Asie
|area= AustralieFrV1
|flux= Pmc
|étape= Corpus
|type= RBID
|clé=
|texte=
}}
| This area was generated with Dilib version V0.6.33. |  |