Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes
Identifieur interne : 000560 ( Ncbi/Curation ); précédent : 000559; suivant : 000561Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes
Auteurs : Narayana M. Upadhyaya [Australie] ; Diana P. Garnica [Australie] ; Haydar Karaoglu [Australie] ; Jana Sperschneider [Australie] ; Adnane Nemri [Australie] ; Bo Xu [Australie] ; Rohit Mago [Australie] ; Christina A. Cuomo [États-Unis] ; John P. Rathjen [Australie] ; Robert F. Park [Australie] ; Jeffrey G. Ellis [Australie] ; Peter N. Dodds [Australie]Source :
- Frontiers in Plant Science [ 1664-462X ] ; 2015.
Abstract
The wheat stem rust fungus
Url:
DOI: 10.3389/fpls.2014.00759
PubMed: 25620970
PubMed Central: 4288056
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Garnica</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Research School of Biology, Australian National University</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Karaoglu, Haydar" sort="Karaoglu, Haydar" uniqKey="Karaoglu H" first="Haydar" last="Karaoglu">Haydar Karaoglu</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Plant Breeding Institute, Faculty of Agriculture and Environment, The University of Sydney</institution><country>Narellan, NSW, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Sperschneider, Jana" sort="Sperschneider, Jana" uniqKey="Sperschneider J" first="Jana" last="Sperschneider">Jana Sperschneider</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Nemri, Adnane" sort="Nemri, Adnane" uniqKey="Nemri A" first="Adnane" last="Nemri">Adnane Nemri</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Xu, Bo" sort="Xu, Bo" uniqKey="Xu B" first="Bo" last="Xu">Bo Xu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Mago, Rohit" sort="Mago, Rohit" uniqKey="Mago R" first="Rohit" last="Mago">Rohit Mago</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Cuomo, Christina A" sort="Cuomo, Christina A" uniqKey="Cuomo C" first="Christina A." last="Cuomo">Christina A. 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Park</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Plant Breeding Institute, Faculty of Agriculture and Environment, The University of Sydney</institution><country>Narellan, NSW, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Ellis, Jeffrey G" sort="Ellis, Jeffrey G" uniqKey="Ellis J" first="Jeffrey G." last="Ellis">Jeffrey G. Ellis</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Dodds, Peter N" sort="Dodds, Peter N" uniqKey="Dodds P" first="Peter N." last="Dodds">Peter N. Dodds</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25620970</idno><idno type="pmc">4288056</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288056</idno><idno type="RBID">PMC:4288056</idno><idno type="doi">10.3389/fpls.2014.00759</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000825</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000825</idno><idno type="wicri:Area/Pmc/Curation">000825</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000825</idno><idno type="wicri:Area/Pmc/Checkpoint">000723</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000723</idno><idno type="wicri:Area/Ncbi/Merge">000560</idno><idno type="wicri:Area/Ncbi/Curation">000560</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comparative genomics of Australian isolates of the wheat stem rust pathogen <italic>Puccinia graminis</italic> f. sp. <italic>tritici</italic> reveals extensive polymorphism in candidate effector genes</title><author><name sortKey="Upadhyaya, Narayana M" sort="Upadhyaya, Narayana M" uniqKey="Upadhyaya N" first="Narayana M." last="Upadhyaya">Narayana M. Upadhyaya</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Garnica, Diana P" sort="Garnica, Diana P" uniqKey="Garnica D" first="Diana P." last="Garnica">Diana P. Garnica</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Research School of Biology, Australian National University</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Karaoglu, Haydar" sort="Karaoglu, Haydar" uniqKey="Karaoglu H" first="Haydar" last="Karaoglu">Haydar Karaoglu</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Plant Breeding Institute, Faculty of Agriculture and Environment, The University of Sydney</institution><country>Narellan, NSW, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Sperschneider, Jana" sort="Sperschneider, Jana" uniqKey="Sperschneider J" first="Jana" last="Sperschneider">Jana Sperschneider</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Nemri, Adnane" sort="Nemri, Adnane" uniqKey="Nemri A" first="Adnane" last="Nemri">Adnane Nemri</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Xu, Bo" sort="Xu, Bo" uniqKey="Xu B" first="Bo" last="Xu">Bo Xu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Mago, Rohit" sort="Mago, Rohit" uniqKey="Mago R" first="Rohit" last="Mago">Rohit Mago</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Cuomo, Christina A" sort="Cuomo, Christina A" uniqKey="Cuomo C" first="Christina A." last="Cuomo">Christina A. Cuomo</name><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard</institution><country>Cambridge, MA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Rathjen, John P" sort="Rathjen, John P" uniqKey="Rathjen J" first="John P." last="Rathjen">John P. Rathjen</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Research School of Biology, Australian National University</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Park, Robert F" sort="Park, Robert F" uniqKey="Park R" first="Robert F." last="Park">Robert F. Park</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Plant Breeding Institute, Faculty of Agriculture and Environment, The University of Sydney</institution><country>Narellan, NSW, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Ellis, Jeffrey G" sort="Ellis, Jeffrey G" uniqKey="Ellis J" first="Jeffrey G." last="Ellis">Jeffrey G. Ellis</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Dodds, Peter N" sort="Dodds, Peter N" uniqKey="Dodds P" first="Peter N." last="Dodds">Peter N. Dodds</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization</institution><country>Canberra, ACT, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The wheat stem rust fungus <italic>Puccinia graminis</italic> f. sp. <italic>tritici</italic> (<italic>Pgt</italic>) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian <italic>Pgt</italic> isolate of pathotype (pt.) 21-0 (collected in 1954) by next generation DNA sequencing. A combination of reference-based assembly using the genome of the previously sequenced American <italic>Pgt</italic> isolate CDL 75-36-700-3 (p7a) and <italic>de novo</italic> assembly were performed resulting in a 92 Mbp reference genome for <italic>Pgt</italic> isolate 21-0. Approximately 13 Mbp of <italic>de novo</italic> assembled sequence in this genome is not present in the p7a reference assembly. This novel sequence is not specific to 21-0 as it is also present in three other <italic>Pgt</italic> rust isolates of independent origin. The new reference genome was subsequently used to build a pan-genome based on five Australian <italic>Pgt</italic> isolates. Transcriptomes from germinated urediniospores and haustoria were separately assembled for pt. 21-0 and comparison of gene expression profiles showed differential expression in ∼10% of the genes each in germinated spores and haustoria. A total of 1,924 secreted proteins were predicted from the 21-0 transcriptome, of which 520 were classified as haustorial secreted proteins (HSPs). Comparison of 21-0 with two presumed clonal field derivatives of this lineage (collected in 1982 and 1984) that had evolved virulence on four additional resistance genes (<italic>Sr5</italic>, <italic>Sr11</italic>, <italic>Sr27</italic>, <italic>SrSatu</italic>) identified mutations in 25 HSP effector candidates. Some of these mutations could explain their novel virulence phenotypes.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Barrett, L G" uniqKey="Barrett L">L. G. Barrett</name></author><author><name sortKey="Thrall, P H" uniqKey="Thrall P">P. H. Thrall</name></author><author><name sortKey="Dodds, P N" uniqKey="Dodds P">P. N. 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