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Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes

Upadhyaya, Narayana M; Garnica, Diana P; Karaoglu, Haydar; Sperschneider, Jana; Nemri, Adnane; Xu, Bo; Mago, Rohit; Cuomo, Christina A; Rathjen, John P; Park, Robert F; Ellis, Jeffrey G; Dodds, Peter N

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The wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian Pgt 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 Pgt isolate CDL 75-36-700-3 (p7a) and de novo assembly were performed resulting in a 92 Mbp reference genome for Pgt isolate 21-0....[Show more]

dc.contributor.authorUpadhyaya, Narayana M
dc.contributor.authorGarnica, Diana P
dc.contributor.authorKaraoglu, Haydar
dc.contributor.authorSperschneider, Jana
dc.contributor.authorNemri, Adnane
dc.contributor.authorXu, Bo
dc.contributor.authorMago, Rohit
dc.contributor.authorCuomo, Christina A
dc.contributor.authorRathjen, John P
dc.contributor.authorPark, Robert F
dc.contributor.authorEllis, Jeffrey G
dc.contributor.authorDodds, Peter N
dc.date.accessioned2015-05-21T02:56:55Z
dc.date.available2015-05-21T02:56:55Z
dc.identifier.issn1664-462X
dc.identifier.urihttp://hdl.handle.net/1885/13544
dc.description.abstractThe wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian Pgt 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 Pgt isolate CDL 75-36-700-3 (p7a) and de novo assembly were performed resulting in a 92 Mbp reference genome for Pgt isolate 21-0. Approximately 13 Mbp of de novo 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 Pgt rust isolates of independent origin. The new reference genome was subsequently used to build a pan-genome based on five Australian Pgt 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 (Sr5, Sr11, Sr27, SrSatu) identified mutations in 25 HSP effector candidates. Some of these mutations could explain their novel virulence phenotypes.
dc.description.sponsorshipAuthors wish to thank the Two Blades Foundation for financial support. Part of this work was supported through access to facilities managed by Bioplatforms Australia and funded by the Australian Government National Collaborative Research Infrastructure Strategy and Education Investment Fund Super Science Initiative.
dc.format13 pages
dc.publisherFrontiers
dc.rights© 2015 Upadhyaya, Garnica, Karaoglu, Sperschneider, Nemri, Xu, Mago, Cuomo, Rathjen, Park, Ellis and Dodds. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
dc.sourceFrontiers in Plant Science
dc.subjectavirulence
dc.subjecteffectors
dc.subjecthaustoria
dc.subjectresistance
dc.subjectsecreted proteins
dc.titleComparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes
dc.typeJournal article
local.identifier.citationvolume5
dcterms.dateAccepted2014-12-09
dc.date.issued2015-01-08
local.identifier.absfor060704 - Plant Pathology
local.identifier.ariespublicationa383154xPUB939
local.publisher.urlhttp://www.frontiersin.org/
local.type.statusPublished Version
local.contributor.affiliationGarnica, Diana P., Division of Plant Sciences, CMBE Research School of Biology, The Australian National University
local.contributor.affiliationRathjen, John P., Division of Plant Sciences, CMBE Research School of Biology, The Australian National University
local.identifier.essn1664-462X
local.bibliographicCitation.issue759
local.bibliographicCitation.startpage1
local.bibliographicCitation.lastpage13
local.identifier.doi10.3389/fpls.2014.00759
local.identifier.absseo820507 - Wheat
dc.date.updated2015-12-10T09:39:37Z
local.identifier.scopusID2-s2.0-84922253019
CollectionsANU Research Publications

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