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 : 000106 ( Main/Exploration ); précédent : 000105; suivant : 000107Comparative 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 ] ; 2014.
Abstract
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. 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.
DOI: 10.3389/fpls.2014.00759
PubMed: 25620970
PubMed Central: PMC4288056
Affiliations:
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Upadhyaya</name><affiliation wicri:level="1"><nlm:affiliation>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></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:affiliation>Research School of Biology, Australian National University Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Research School of Biology, Australian National University Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></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:affiliation>Plant Breeding Institute, Faculty of Agriculture and Environment, The University of Sydney Narellan, NSW, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Plant Breeding Institute, Faculty of Agriculture and Environment, The University of Sydney Narellan, NSW</wicri:regionArea><wicri:noRegion>NSW</wicri:noRegion></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:affiliation>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></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:affiliation>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></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:affiliation>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></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:affiliation>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></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="2"><nlm:affiliation>Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard Cambridge, MA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard Cambridge, MA</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></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:affiliation>Research School of Biology, Australian National University Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Research School of Biology, Australian National University Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></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:affiliation>Plant Breeding Institute, Faculty of Agriculture and Environment, The University of Sydney Narellan, NSW, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Plant Breeding Institute, Faculty of Agriculture and Environment, The University of Sydney Narellan, NSW</wicri:regionArea><wicri:noRegion>NSW</wicri:noRegion></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:affiliation>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></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:affiliation>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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. 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. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">25620970</PMID><DateCompleted><Year>2015</Year><Month>01</Month><Day>26</Day></DateCompleted><DateRevised><Year>2020</Year><Month>10</Month><Day>01</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes.</ArticleTitle><Pagination><MedlinePgn>759</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2014.00759</ELocationID><Abstract><AbstractText>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. 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. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Upadhyaya</LastName><ForeName>Narayana M</ForeName><Initials>NM</Initials><AffiliationInfo><Affiliation>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Garnica</LastName><ForeName>Diana P</ForeName><Initials>DP</Initials><AffiliationInfo><Affiliation>Research School of Biology, Australian National University Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Karaoglu</LastName><ForeName>Haydar</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Plant Breeding Institute, Faculty of Agriculture and Environment, The University of Sydney Narellan, NSW, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sperschneider</LastName><ForeName>Jana</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nemri</LastName><ForeName>Adnane</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Bo</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mago</LastName><ForeName>Rohit</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cuomo</LastName><ForeName>Christina A</ForeName><Initials>CA</Initials><AffiliationInfo><Affiliation>Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard Cambridge, MA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rathjen</LastName><ForeName>John P</ForeName><Initials>JP</Initials><AffiliationInfo><Affiliation>Research School of Biology, Australian National University Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Park</LastName><ForeName>Robert F</ForeName><Initials>RF</Initials><AffiliationInfo><Affiliation>Plant Breeding Institute, Faculty of Agriculture and Environment, The University of Sydney Narellan, NSW, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ellis</LastName><ForeName>Jeffrey G</ForeName><Initials>JG</Initials><AffiliationInfo><Affiliation>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dodds</LastName><ForeName>Peter N</ForeName><Initials>PN</Initials><AffiliationInfo><Affiliation>Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>01</Month><Day>08</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">avirulence</Keyword><Keyword MajorTopicYN="N">effectors</Keyword><Keyword MajorTopicYN="N">haustoria</Keyword><Keyword MajorTopicYN="N">resistance</Keyword><Keyword MajorTopicYN="N">secreted proteins</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>05</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>12</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>1</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>1</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>1</Month><Day>27</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25620970</ArticleId><ArticleId 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Upadhyaya</name></noRegion><name sortKey="Dodds, Peter N" sort="Dodds, Peter N" uniqKey="Dodds P" first="Peter N" last="Dodds">Peter N. Dodds</name><name sortKey="Ellis, Jeffrey G" sort="Ellis, Jeffrey G" uniqKey="Ellis J" first="Jeffrey G" last="Ellis">Jeffrey G. Ellis</name><name sortKey="Garnica, Diana P" sort="Garnica, Diana P" uniqKey="Garnica D" first="Diana P" last="Garnica">Diana P. Garnica</name><name sortKey="Karaoglu, Haydar" sort="Karaoglu, Haydar" uniqKey="Karaoglu H" first="Haydar" last="Karaoglu">Haydar Karaoglu</name><name sortKey="Mago, Rohit" sort="Mago, Rohit" uniqKey="Mago R" first="Rohit" last="Mago">Rohit Mago</name><name sortKey="Nemri, Adnane" sort="Nemri, Adnane" uniqKey="Nemri A" first="Adnane" last="Nemri">Adnane Nemri</name><name sortKey="Park, Robert F" sort="Park, Robert F" uniqKey="Park R" first="Robert F" last="Park">Robert F. Park</name><name sortKey="Rathjen, John P" sort="Rathjen, John P" uniqKey="Rathjen J" first="John P" last="Rathjen">John P. Rathjen</name><name sortKey="Sperschneider, Jana" sort="Sperschneider, Jana" uniqKey="Sperschneider J" first="Jana" last="Sperschneider">Jana Sperschneider</name><name sortKey="Xu, Bo" sort="Xu, Bo" uniqKey="Xu B" first="Bo" last="Xu">Bo Xu</name></country><country name="États-Unis"><region name="Massachusetts"><name sortKey="Cuomo, Christina A" sort="Cuomo, Christina A" uniqKey="Cuomo C" first="Christina A" last="Cuomo">Christina A. Cuomo</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|texte= Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes.
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