Identification of Avramr1 from Phytophthora infestans using long read and cDNA pathogen-enrichment sequencing (PenSeq).
Identifieur interne : 000137 ( Main/Exploration ); précédent : 000136; suivant : 000138Identification of Avramr1 from Phytophthora infestans using long read and cDNA pathogen-enrichment sequencing (PenSeq).
Auteurs : Xiao Lin [Royaume-Uni] ; Tianqiao Song [Royaume-Uni] ; Sebastian Fairhead [Royaume-Uni] ; Kamil Witek [Royaume-Uni] ; Agathe Jouet [Royaume-Uni] ; Florian Jupe [Royaume-Uni] ; Agnieszka I. Witek [Royaume-Uni] ; Hari S. Karki [Royaume-Uni] ; Vivianne G A A. Vleeshouwers [Pays-Bas] ; Ingo Hein [Royaume-Uni] ; Jonathan D G. Jones [Royaume-Uni]Source :
- Molecular plant pathology [ 1364-3703 ] ; 2020.
Abstract
Potato late blight, caused by the oomycete pathogen Phytophthora infestans, significantly hampers potato production. Recently, a new Resistance to Phytophthora infestans (Rpi) gene, Rpi-amr1, was cloned from a wild Solanum species, Solanum americanum. Identification of the corresponding recognized effector (Avirulence or Avr) genes from P. infestans is key to elucidating their naturally occurring sequence variation, which in turn informs the potential durability of the cognate late blight resistance. To identify the P. infestans effector recognized by Rpi-amr1, we screened available RXLR effector libraries and used long read and cDNA pathogen-enrichment sequencing (PenSeq) on four P. infestans isolates to explore the untested effectors. Using single-molecule real-time sequencing (SMRT) and cDNA PenSeq, we identified 47 highly expressed effectors from P. infestans, including PITG_07569, which triggers a highly specific cell death response when transiently coexpressed with Rpi-amr1 in Nicotiana benthamiana, suggesting that PITG_07569 is Avramr1. Here we demonstrate that long read and cDNA PenSeq enables the identification of full-length RXLR effector families and their expression profile. This study has revealed key insights into the evolution and polymorphism of a complex RXLR effector family that is associated with the recognition by Rpi-amr1.
DOI: 10.1111/mpp.12987
PubMed: 32935441
PubMed Central: PMC7548994
Affiliations:
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Witek</name><affiliation wicri:level="1"><nlm:affiliation>The Sainsbury Laboratory, University of East Anglia, Norwich, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Sainsbury Laboratory, University of East Anglia, Norwich</wicri:regionArea><wicri:noRegion>Norwich</wicri:noRegion></affiliation></author><author><name sortKey="Karki, Hari S" sort="Karki, Hari S" uniqKey="Karki H" first="Hari S" last="Karki">Hari S. Karki</name><affiliation wicri:level="1"><nlm:affiliation>The Sainsbury Laboratory, University of East Anglia, Norwich, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Sainsbury Laboratory, University of East Anglia, Norwich</wicri:regionArea><wicri:noRegion>Norwich</wicri:noRegion></affiliation></author><author><name sortKey="Vleeshouwers, Vivianne G A A" sort="Vleeshouwers, Vivianne G A A" uniqKey="Vleeshouwers V" first="Vivianne G A A" last="Vleeshouwers">Vivianne G A A. Vleeshouwers</name><affiliation wicri:level="1"><nlm:affiliation>Plant Breeding, Wageningen University and Research, Wageningen, Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Plant Breeding, Wageningen University and Research, Wageningen</wicri:regionArea><wicri:noRegion>Wageningen</wicri:noRegion></affiliation></author><author><name sortKey="Hein, Ingo" sort="Hein, Ingo" uniqKey="Hein I" first="Ingo" last="Hein">Ingo Hein</name><affiliation wicri:level="1"><nlm:affiliation>School of Life Sciences, Division of Plant Sciences, University of Dundee, Dundee, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>School of Life Sciences, Division of Plant Sciences, University of Dundee, Dundee</wicri:regionArea><wicri:noRegion>Dundee</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee</wicri:regionArea><wicri:noRegion>Dundee</wicri:noRegion></affiliation></author><author><name sortKey="Jones, Jonathan D G" sort="Jones, Jonathan D G" uniqKey="Jones J" first="Jonathan D G" last="Jones">Jonathan D G. Jones</name><affiliation wicri:level="1"><nlm:affiliation>The Sainsbury Laboratory, University of East Anglia, Norwich, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Sainsbury Laboratory, University of East Anglia, Norwich</wicri:regionArea><wicri:noRegion>Norwich</wicri:noRegion></affiliation></author></analytic><series><title level="j">Molecular plant pathology</title><idno type="eISSN">1364-3703</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Potato late blight, caused by the oomycete pathogen Phytophthora infestans, significantly hampers potato production. Recently, a new Resistance to Phytophthora infestans (Rpi) gene, Rpi-amr1, was cloned from a wild Solanum species, Solanum americanum. Identification of the corresponding recognized effector (Avirulence or Avr) genes from P. infestans is key to elucidating their naturally occurring sequence variation, which in turn informs the potential durability of the cognate late blight resistance. To identify the P. infestans effector recognized by Rpi-amr1, we screened available RXLR effector libraries and used long read and cDNA pathogen-enrichment sequencing (PenSeq) on four P. infestans isolates to explore the untested effectors. Using single-molecule real-time sequencing (SMRT) and cDNA PenSeq, we identified 47 highly expressed effectors from P. infestans, including PITG_07569, which triggers a highly specific cell death response when transiently coexpressed with Rpi-amr1 in Nicotiana benthamiana, suggesting that PITG_07569 is Avramr1. Here we demonstrate that long read and cDNA PenSeq enables the identification of full-length RXLR effector families and their expression profile. This study has revealed key insights into the evolution and polymorphism of a complex RXLR effector family that is associated with the recognition by Rpi-amr1.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">32935441</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1364-3703</ISSN><JournalIssue CitedMedium="Internet"><Volume>21</Volume><Issue>11</Issue><PubDate><Year>2020</Year><Month>Nov</Month></PubDate></JournalIssue><Title>Molecular plant pathology</Title><ISOAbbreviation>Mol Plant Pathol</ISOAbbreviation></Journal><ArticleTitle>Identification of Avramr1 from Phytophthora infestans using long read and cDNA pathogen-enrichment sequencing (PenSeq).</ArticleTitle><Pagination><MedlinePgn>1502-1512</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/mpp.12987</ELocationID><Abstract><AbstractText>Potato late blight, caused by the oomycete pathogen Phytophthora infestans, significantly hampers potato production. Recently, a new Resistance to Phytophthora infestans (Rpi) gene, Rpi-amr1, was cloned from a wild Solanum species, Solanum americanum. Identification of the corresponding recognized effector (Avirulence or Avr) genes from P. infestans is key to elucidating their naturally occurring sequence variation, which in turn informs the potential durability of the cognate late blight resistance. To identify the P. infestans effector recognized by Rpi-amr1, we screened available RXLR effector libraries and used long read and cDNA pathogen-enrichment sequencing (PenSeq) on four P. infestans isolates to explore the untested effectors. Using single-molecule real-time sequencing (SMRT) and cDNA PenSeq, we identified 47 highly expressed effectors from P. infestans, including PITG_07569, which triggers a highly specific cell death response when transiently coexpressed with Rpi-amr1 in Nicotiana benthamiana, suggesting that PITG_07569 is Avramr1. Here we demonstrate that long read and cDNA PenSeq enables the identification of full-length RXLR effector families and their expression profile. This study has revealed key insights into the evolution and polymorphism of a complex RXLR effector family that is associated with the recognition by Rpi-amr1.</AbstractText><CopyrightInformation>© 2020 The Authors. Molecular Plant Pathology published by British Society for Plant Pathology and John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lin</LastName><ForeName>Xiao</ForeName><Initials>X</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-3848-0244</Identifier><AffiliationInfo><Affiliation>The Sainsbury Laboratory, University of East Anglia, Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Song</LastName><ForeName>Tianqiao</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>The Sainsbury Laboratory, University of East Anglia, Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fairhead</LastName><ForeName>Sebastian</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>The Sainsbury Laboratory, University of East Anglia, Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Witek</LastName><ForeName>Kamil</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>The Sainsbury Laboratory, University of East Anglia, Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jouet</LastName><ForeName>Agathe</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>The Sainsbury Laboratory, University of East Anglia, Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jupe</LastName><ForeName>Florian</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>The Sainsbury Laboratory, University of East Anglia, Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Witek</LastName><ForeName>Agnieszka I</ForeName><Initials>AI</Initials><AffiliationInfo><Affiliation>The Sainsbury Laboratory, University of East Anglia, Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Karki</LastName><ForeName>Hari S</ForeName><Initials>HS</Initials><AffiliationInfo><Affiliation>The Sainsbury Laboratory, University of East Anglia, Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vleeshouwers</LastName><ForeName>Vivianne G A A</ForeName><Initials>VGAA</Initials><AffiliationInfo><Affiliation>Plant Breeding, Wageningen University and Research, Wageningen, Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hein</LastName><ForeName>Ingo</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>School of Life Sciences, Division of Plant Sciences, University of Dundee, Dundee, UK.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jones</LastName><ForeName>Jonathan D G</ForeName><Initials>JDG</Initials><AffiliationInfo><Affiliation>The Sainsbury Laboratory, University of East Anglia, Norwich, UK.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>BB/P021646/1</GrantID><Acronym>BB_</Acronym><Agency>Biotechnology and Biological Sciences Research Council</Agency><Country>United Kingdom</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>09</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Plant Pathol</MedlineTA><NlmUniqueID>100954969</NlmUniqueID><ISSNLinking>1364-3703</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Avramr1
</Keyword><Keyword MajorTopicYN="N">Phytophthora infestans
</Keyword><Keyword MajorTopicYN="N">Rpi-amr1
</Keyword><Keyword MajorTopicYN="N">PenSeq</Keyword><Keyword MajorTopicYN="N">RXLR effector</Keyword><Keyword MajorTopicYN="N">late blight</Keyword><Keyword MajorTopicYN="N">oomycete</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>06</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>07</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>08</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>9</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>9</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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