Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae.
Identifieur interne : 000270 ( Main/Exploration ); précédent : 000269; suivant : 000271Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae.
Auteurs : Jamie Mcgowan [Irlande (pays)] ; Richard O'Hanlon [Royaume-Uni] ; Rebecca A. Owens [Irlande (pays)] ; David A. Fitzpatrick [Irlande (pays)]Source :
- Microorganisms [ 2076-2607 ] ; 2020.
Abstract
The Phytophthora genus includes some of the most devastating plant pathogens. Here we report draft genome sequences for three ubiquitous Phytophthora species-Phytophthora chlamydospora, Phytophthora gonapodyides, and Phytophthora pseudosyringae. Phytophthora pseudosyringae is an important forest pathogen that is abundant in Europe and North America. Phytophthora chlamydospora and Ph. gonapodyides are globally widespread species often associated with aquatic habitats. They are both regarded as opportunistic plant pathogens. The three sequenced genomes range in size from 45 Mb to 61 Mb. Similar to other oomycete species, tandem gene duplication appears to have played an important role in the expansion of effector arsenals. Comparative analysis of carbohydrate-active enzymes (CAZymes) across 44 oomycete genomes indicates that oomycete lifestyles may be linked to CAZyme repertoires. The mitochondrial genome sequence of each species was also determined, and their gene content and genome structure were compared. Using mass spectrometry, we characterised the extracellular proteome of each species and identified large numbers of proteins putatively involved in pathogenicity and osmotrophy. The mycelial proteome of each species was also characterised using mass spectrometry. In total, the expression of approximately 3000 genes per species was validated at the protein level. These genome resources will be valuable for future studies to understand the behaviour of these three widespread Phytophthora species.
DOI: 10.3390/microorganisms8050653
PubMed: 32365808
PubMed Central: PMC7285336
Affiliations:
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Kildare W23 F2H6, Ireland.</nlm:affiliation><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>Department of Biology, Maynooth University, Maynooth, Co. Kildare W23 F2H6</wicri:regionArea><orgName type="university">Université nationale d'Irlande à Maynooth</orgName><placeName><settlement type="city">Maynooth</settlement><region type="région" nuts="2">Leinster</region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare W23 F2H6, Ireland.</nlm:affiliation><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare W23 F2H6</wicri:regionArea><orgName type="university">Université nationale d'Irlande à Maynooth</orgName><placeName><settlement type="city">Maynooth</settlement><region type="région" nuts="2">Leinster</region></placeName></affiliation></author><author><name sortKey="O Hanlon, Richard" sort="O Hanlon, Richard" uniqKey="O Hanlon R" first="Richard" last="O'Hanlon">Richard O'Hanlon</name><affiliation wicri:level="1"><nlm:affiliation>Agri-Food & Biosciences Institute (AFBI), Belfast BT9 5PX, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Agri-Food & Biosciences Institute (AFBI), Belfast BT9 5PX</wicri:regionArea><wicri:noRegion>Belfast BT9 5PX</wicri:noRegion></affiliation></author><author><name sortKey="Owens, Rebecca A" sort="Owens, Rebecca A" uniqKey="Owens R" first="Rebecca A" last="Owens">Rebecca A. Owens</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biology, Maynooth University, Maynooth, Co. Kildare W23 F2H6, Ireland.</nlm:affiliation><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>Department of Biology, Maynooth University, Maynooth, Co. Kildare W23 F2H6</wicri:regionArea><orgName type="university">Université nationale d'Irlande à Maynooth</orgName><placeName><settlement type="city">Maynooth</settlement><region type="région" nuts="2">Leinster</region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare W23 F2H6, Ireland.</nlm:affiliation><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare W23 F2H6</wicri:regionArea><orgName type="university">Université nationale d'Irlande à Maynooth</orgName><placeName><settlement type="city">Maynooth</settlement><region type="région" nuts="2">Leinster</region></placeName></affiliation></author><author><name sortKey="Fitzpatrick, David A" sort="Fitzpatrick, David A" uniqKey="Fitzpatrick D" first="David A" last="Fitzpatrick">David A. Fitzpatrick</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biology, Maynooth University, Maynooth, Co. Kildare W23 F2H6, Ireland.</nlm:affiliation><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>Department of Biology, Maynooth University, Maynooth, Co. Kildare W23 F2H6</wicri:regionArea><orgName type="university">Université nationale d'Irlande à Maynooth</orgName><placeName><settlement type="city">Maynooth</settlement><region type="région" nuts="2">Leinster</region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare W23 F2H6, Ireland.</nlm:affiliation><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare W23 F2H6</wicri:regionArea><orgName type="university">Université nationale d'Irlande à Maynooth</orgName><placeName><settlement type="city">Maynooth</settlement><region type="région" nuts="2">Leinster</region></placeName></affiliation></author></analytic><series><title level="j">Microorganisms</title><idno type="ISSN">2076-2607</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">The <i>Phytophthora</i> genus includes some of the most devastating plant pathogens. Here we report draft genome sequences for three ubiquitous <i>Phytophthora</i> species-<i>Phytophthora chlamydospora</i>, <i>Phytophthora gonapodyides</i>, and <i>Phytophthora pseudosyringae</i>. <i>Phytophthora pseudosyringae</i> is an important forest pathogen that is abundant in Europe and North America. <i>Phytophthora chlamydospora</i> and <i>Ph. gonapodyides</i> are globally widespread species often associated with aquatic habitats. They are both regarded as opportunistic plant pathogens. The three sequenced genomes range in size from 45 Mb to 61 Mb. Similar to other oomycete species, tandem gene duplication appears to have played an important role in the expansion of effector arsenals. Comparative analysis of carbohydrate-active enzymes (CAZymes) across 44 oomycete genomes indicates that oomycete lifestyles may be linked to CAZyme repertoires. The mitochondrial genome sequence of each species was also determined, and their gene content and genome structure were compared. Using mass spectrometry, we characterised the extracellular proteome of each species and identified large numbers of proteins putatively involved in pathogenicity and osmotrophy. The mycelial proteome of each species was also characterised using mass spectrometry. In total, the expression of approximately 3000 genes per species was validated at the protein level. These genome resources will be valuable for future studies to understand the behaviour of these three widespread <i>Phytophthora</i> species.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32365808</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>28</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Print">2076-2607</ISSN><JournalIssue CitedMedium="Print"><Volume>8</Volume><Issue>5</Issue><PubDate><Year>2020</Year><Month>Apr</Month><Day>30</Day></PubDate></JournalIssue><Title>Microorganisms</Title><ISOAbbreviation>Microorganisms</ISOAbbreviation></Journal><ArticleTitle>Comparative Genomic and Proteomic Analyses of Three Widespread <i>Phytophthora</i> Species: <i>Phytophthora chlamydospora</i>, <i>Phytophthora gonapodyides</i> and <i>Phytophthora pseudosyringae</i>.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">E653</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.3390/microorganisms8050653</ELocationID><Abstract><AbstractText>The <i>Phytophthora</i> genus includes some of the most devastating plant pathogens. Here we report draft genome sequences for three ubiquitous <i>Phytophthora</i> species-<i>Phytophthora chlamydospora</i>, <i>Phytophthora gonapodyides</i>, and <i>Phytophthora pseudosyringae</i>. <i>Phytophthora pseudosyringae</i> is an important forest pathogen that is abundant in Europe and North America. <i>Phytophthora chlamydospora</i> and <i>Ph. gonapodyides</i> are globally widespread species often associated with aquatic habitats. They are both regarded as opportunistic plant pathogens. The three sequenced genomes range in size from 45 Mb to 61 Mb. Similar to other oomycete species, tandem gene duplication appears to have played an important role in the expansion of effector arsenals. Comparative analysis of carbohydrate-active enzymes (CAZymes) across 44 oomycete genomes indicates that oomycete lifestyles may be linked to CAZyme repertoires. The mitochondrial genome sequence of each species was also determined, and their gene content and genome structure were compared. Using mass spectrometry, we characterised the extracellular proteome of each species and identified large numbers of proteins putatively involved in pathogenicity and osmotrophy. The mycelial proteome of each species was also characterised using mass spectrometry. In total, the expression of approximately 3000 genes per species was validated at the protein level. These genome resources will be valuable for future studies to understand the behaviour of these three widespread <i>Phytophthora</i> species.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>McGowan</LastName><ForeName>Jamie</ForeName><Initials>J</Initials><Identifier Source="ORCID">0000-0002-4240-5175</Identifier><AffiliationInfo><Affiliation>Department of Biology, Maynooth University, Maynooth, Co. Kildare W23 F2H6, Ireland.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare W23 F2H6, Ireland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>O'Hanlon</LastName><ForeName>Richard</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Agri-Food & Biosciences Institute (AFBI), Belfast BT9 5PX, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Owens</LastName><ForeName>Rebecca A</ForeName><Initials>RA</Initials><AffiliationInfo><Affiliation>Department of Biology, Maynooth University, Maynooth, Co. Kildare W23 F2H6, Ireland.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare W23 F2H6, Ireland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fitzpatrick</LastName><ForeName>David A</ForeName><Initials>DA</Initials><Identifier Source="ORCID">0000-0001-7345-6998</Identifier><AffiliationInfo><Affiliation>Department of Biology, Maynooth University, Maynooth, Co. Kildare W23 F2H6, Ireland.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare W23 F2H6, Ireland.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>GOIPG/2016/1112</GrantID><Agency>Irish Research Council</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>04</Month><Day>30</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Microorganisms</MedlineTA><NlmUniqueID>101625893</NlmUniqueID><ISSNLinking>2076-2607</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">comparative genomics</Keyword><Keyword MajorTopicYN="N">effectors</Keyword><Keyword MajorTopicYN="N">extracellular proteome</Keyword><Keyword MajorTopicYN="N">genome evolution</Keyword><Keyword MajorTopicYN="N">mass spectrometry</Keyword><Keyword MajorTopicYN="N">phylogenomics</Keyword><Keyword MajorTopicYN="N">phytophthora proteomics</Keyword><Keyword MajorTopicYN="N">plant pathogen</Keyword><Keyword MajorTopicYN="N">secretome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>04</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>04</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>04</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>5</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>5</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>5</Month><Day>6</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId 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Fitzpatrick</name><name sortKey="Fitzpatrick, David A" sort="Fitzpatrick, David A" uniqKey="Fitzpatrick D" first="David A" last="Fitzpatrick">David A. Fitzpatrick</name><name sortKey="Mcgowan, Jamie" sort="Mcgowan, Jamie" uniqKey="Mcgowan J" first="Jamie" last="Mcgowan">Jamie Mcgowan</name><name sortKey="Owens, Rebecca A" sort="Owens, Rebecca A" uniqKey="Owens R" first="Rebecca A" last="Owens">Rebecca A. Owens</name><name sortKey="Owens, Rebecca A" sort="Owens, Rebecca A" uniqKey="Owens R" first="Rebecca A" last="Owens">Rebecca A. Owens</name></country><country name="Royaume-Uni"><noRegion><name sortKey="O Hanlon, Richard" sort="O Hanlon, Richard" uniqKey="O Hanlon R" first="Richard" last="O'Hanlon">Richard O'Hanlon</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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