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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PMC:4288056Le document en format XML
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f. sp. <italic>tritici</italic>
reveals extensive polymorphism in candidate effector genes</title>
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<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>
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<author><name sortKey="Garnica, Diana P" sort="Garnica, Diana P" uniqKey="Garnica D" first="Diana P." last="Garnica">Diana P. Garnica</name>
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<author><name sortKey="Karaoglu, Haydar" sort="Karaoglu, Haydar" uniqKey="Karaoglu H" first="Haydar" last="Karaoglu">Haydar Karaoglu</name>
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<country>Canberra, ACT, Australia</country>
</nlm:aff>
<country xml:lang="fr">Australie</country>
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</affiliation>
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<author><name sortKey="Nemri, Adnane" sort="Nemri, Adnane" uniqKey="Nemri A" first="Adnane" last="Nemri">Adnane Nemri</name>
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<country>Canberra, ACT, Australia</country>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea></wicri:regionArea>
</affiliation>
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<author><name sortKey="Xu, Bo" sort="Xu, Bo" uniqKey="Xu B" first="Bo" last="Xu">Bo Xu</name>
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<country>Canberra, ACT, Australia</country>
</nlm:aff>
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<author><name sortKey="Mago, Rohit" sort="Mago, Rohit" uniqKey="Mago R" first="Rohit" last="Mago">Rohit Mago</name>
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<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>
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<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>
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<author><name sortKey="Park, Robert F" sort="Park, Robert F" uniqKey="Park R" first="Robert F." last="Park">Robert F. Park</name>
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<country>Narellan, NSW, Australia</country>
</nlm:aff>
<country xml:lang="fr">Australie</country>
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</affiliation>
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<author><name sortKey="Ellis, Jeffrey G" sort="Ellis, Jeffrey G" uniqKey="Ellis J" first="Jeffrey G." last="Ellis">Jeffrey G. Ellis</name>
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<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>
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<series><title level="j">Frontiers in Plant Science</title>
<idno type="eISSN">1664-462X</idno>
<imprint><date when="2015">2015</date>
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<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>
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