Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii.
Identifieur interne : 000147 ( Main/Exploration ); précédent : 000146; suivant : 000148Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii.
Auteurs : Peter Henry [États-Unis] ; Sukhwinder Kaur [États-Unis] ; Quyen Anh Tran Pham [États-Unis] ; Radwan Barakat [États-Unis] ; Samuel Brinker [États-Unis] ; Hannah Haensel [États-Unis] ; Oleg Daugovish [États-Unis] ; Lynn Epstein [États-Unis]Source :
- BMC genomics [ 1471-2164 ] ; 2020.
Abstract
BACKGROUND
Members of the F. oxysporium species complex (FOSC) in the f. sp. apii (Foa) are pathogenic on celery and those in f. sp. coriandrii (Foci) are pathogenic on coriander (=cilantro). Foci was first reported in California in 2005; a new and highly aggressive race 4 of Foa was observed in 2013 in California. Preliminary evidence indicated that Foa can also cause disease on coriander, albeit are less virulent than Foci. Comparative genomics was used to investigate the evolutionary relationships between Foa race 4, Foa race 3, and the Foci, which are all in FOSC Clade 2, and Foa race 2, which is in FOSC Clade 3.
RESULTS
A phylogenetic analysis of 2718 single-copy conserved genes and mitochondrial DNA sequence indicated that Foa races 3 and 4 and the Foci are monophyletic within FOSC Clade 2; these strains also are in a single somatic compatibility group. However, in the accessory genomes, the Foci versus Foa races 3 and 4 differ in multiple contigs. Based on significantly increased expression of Foa race 4 genes in planta vs. in vitro, we identified 23 putative effectors and 13 possible pathogenicity factors. PCR primers for diagnosis of either Foa race 2 or 4 and the Foci were identified. Finally, mixtures of conidia that were pre-stained with different fluorochromes indicated that Foa race 4 formed conidial anastomosis tubes (CATs) with Foci. Foa race 4 and Foa race 2, which are in different somatic compatibility groups, did not form CATs with each other.
CONCLUSIONS
There was no evidence that Foa race 2 was involved in the recent evolution of Foa race 4; Foa race 2 and 4 are CAT-incompatible. Although Foa races 3 and 4 and the Foci are closely related, there is no evidence that either Foci contributed to the evolution of Foa race 4, or that Foa race 4 was the recent recipient of a multi-gene chromosomal segment from another strain. However, horizontal chromosome transfer could account for the major difference in the accessory genomes of Foa race 4 and the Foci and for their differences in host range.
DOI: 10.1186/s12864-020-07141-5
PubMed: 33081696
PubMed Central: PMC7576743
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii.</title><author><name sortKey="Henry, Peter" sort="Henry, Peter" uniqKey="Henry P" first="Peter" last="Henry">Peter Henry</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of California, Davis, California, 95616-8680</wicri:regionArea><wicri:noRegion>95616-8680</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>USDA-ARS, 1636 East Alisal St., Salinas, CA, 93905, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, 1636 East Alisal St., Salinas, CA, 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wicri:level="1"><nlm:affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of California, Davis, California, 95616-8680</wicri:regionArea><wicri:noRegion>95616-8680</wicri:noRegion></affiliation></author><author><name sortKey="Daugovish, Oleg" sort="Daugovish, Oleg" uniqKey="Daugovish O" first="Oleg" last="Daugovish">Oleg Daugovish</name><affiliation wicri:level="1"><nlm:affiliation>University of California Cooperative Extension, 669 County Square Drive, Suite 100, Ventura, CA, 93003, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>University of California Cooperative Extension, 669 County Square Drive, Suite 100, Ventura, CA, 93003</wicri:regionArea><wicri:noRegion>93003</wicri:noRegion></affiliation></author><author><name sortKey="Epstein, Lynn" sort="Epstein, Lynn" uniqKey="Epstein L" first="Lynn" last="Epstein">Lynn Epstein</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA. lepstein@ucdavis.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of California, Davis, California, 95616-8680</wicri:regionArea><wicri:noRegion>95616-8680</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:33081696</idno><idno type="pmid">33081696</idno><idno type="doi">10.1186/s12864-020-07141-5</idno><idno type="pmc">PMC7576743</idno><idno type="wicri:Area/Main/Corpus">000053</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000053</idno><idno type="wicri:Area/Main/Curation">000053</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000053</idno><idno type="wicri:Area/Main/Exploration">000053</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii.</title><author><name sortKey="Henry, Peter" sort="Henry, Peter" uniqKey="Henry P" first="Peter" last="Henry">Peter Henry</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of California, Davis, California, 95616-8680</wicri:regionArea><wicri:noRegion>95616-8680</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>USDA-ARS, 1636 East Alisal St., Salinas, CA, 93905, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, 1636 East Alisal St., Salinas, CA, 93905</wicri:regionArea><wicri:noRegion>93905</wicri:noRegion></affiliation></author><author><name sortKey="Kaur, Sukhwinder" sort="Kaur, Sukhwinder" uniqKey="Kaur S" first="Sukhwinder" last="Kaur">Sukhwinder Kaur</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of California, Davis, California, 95616-8680</wicri:regionArea><wicri:noRegion>95616-8680</wicri:noRegion></affiliation></author><author><name sortKey="Pham, Quyen Anh Tran" sort="Pham, Quyen Anh Tran" uniqKey="Pham Q" first="Quyen Anh Tran" last="Pham">Quyen Anh Tran Pham</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of California, Davis, California, 95616-8680</wicri:regionArea><wicri:noRegion>95616-8680</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Current address: Janssen Biopharma, Inc., 260 E Grand Ave., South San Francisco, CA, 94080, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Current address: Janssen Biopharma, Inc., 260 E Grand Ave., South San Francisco, CA, 94080</wicri:regionArea><wicri:noRegion>94080</wicri:noRegion></affiliation></author><author><name sortKey="Barakat, Radwan" sort="Barakat, Radwan" uniqKey="Barakat R" first="Radwan" last="Barakat">Radwan Barakat</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of California, Davis, California, 95616-8680</wicri:regionArea><wicri:noRegion>95616-8680</wicri:noRegion></affiliation><affiliation><nlm:affiliation>Department of Plant Production & Protection, College of Agriculture, Hebron University, Hebron, Palestine.</nlm:affiliation><wicri:noCountry code="subField">Palestine</wicri:noCountry></affiliation></author><author><name sortKey="Brinker, Samuel" sort="Brinker, Samuel" uniqKey="Brinker S" first="Samuel" last="Brinker">Samuel Brinker</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of California, Davis, California, 95616-8680</wicri:regionArea><wicri:noRegion>95616-8680</wicri:noRegion></affiliation></author><author><name sortKey="Haensel, Hannah" sort="Haensel, Hannah" uniqKey="Haensel H" first="Hannah" last="Haensel">Hannah Haensel</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of California, Davis, California, 95616-8680</wicri:regionArea><wicri:noRegion>95616-8680</wicri:noRegion></affiliation></author><author><name sortKey="Daugovish, Oleg" sort="Daugovish, Oleg" uniqKey="Daugovish O" first="Oleg" last="Daugovish">Oleg Daugovish</name><affiliation wicri:level="1"><nlm:affiliation>University of California Cooperative Extension, 669 County Square Drive, Suite 100, Ventura, CA, 93003, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>University of California Cooperative Extension, 669 County Square Drive, Suite 100, Ventura, CA, 93003</wicri:regionArea><wicri:noRegion>93003</wicri:noRegion></affiliation></author><author><name sortKey="Epstein, Lynn" sort="Epstein, Lynn" uniqKey="Epstein L" first="Lynn" last="Epstein">Lynn Epstein</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA. lepstein@ucdavis.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of California, Davis, California, 95616-8680</wicri:regionArea><wicri:noRegion>95616-8680</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</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"><p><b>BACKGROUND</b></p><p>Members of the F. oxysporium species complex (FOSC) in the f. sp. apii (Foa) are pathogenic on celery and those in f. sp. coriandrii (Foci) are pathogenic on coriander (=cilantro). Foci was first reported in California in 2005; a new and highly aggressive race 4 of Foa was observed in 2013 in California. Preliminary evidence indicated that Foa can also cause disease on coriander, albeit are less virulent than Foci. Comparative genomics was used to investigate the evolutionary relationships between Foa race 4, Foa race 3, and the Foci, which are all in FOSC Clade 2, and Foa race 2, which is in FOSC Clade 3.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>A phylogenetic analysis of 2718 single-copy conserved genes and mitochondrial DNA sequence indicated that Foa races 3 and 4 and the Foci are monophyletic within FOSC Clade 2; these strains also are in a single somatic compatibility group. However, in the accessory genomes, the Foci versus Foa races 3 and 4 differ in multiple contigs. Based on significantly increased expression of Foa race 4 genes in planta vs. in vitro, we identified 23 putative effectors and 13 possible pathogenicity factors. PCR primers for diagnosis of either Foa race 2 or 4 and the Foci were identified. Finally, mixtures of conidia that were pre-stained with different fluorochromes indicated that Foa race 4 formed conidial anastomosis tubes (CATs) with Foci. Foa race 4 and Foa race 2, which are in different somatic compatibility groups, did not form CATs with each other.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>There was no evidence that Foa race 2 was involved in the recent evolution of Foa race 4; Foa race 2 and 4 are CAT-incompatible. Although Foa races 3 and 4 and the Foci are closely related, there is no evidence that either Foci contributed to the evolution of Foa race 4, or that Foa race 4 was the recent recipient of a multi-gene chromosomal segment from another strain. However, horizontal chromosome transfer could account for the major difference in the accessory genomes of Foa race 4 and the Foci and for their differences in host range.</p></div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">33081696</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>24</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>21</Volume><Issue>1</Issue><PubDate><Year>2020</Year><Month>Oct</Month><Day>20</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii.</ArticleTitle><Pagination><MedlinePgn>730</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-020-07141-5</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Members of the F. oxysporium species complex (FOSC) in the f. sp. apii (Foa) are pathogenic on celery and those in f. sp. coriandrii (Foci) are pathogenic on coriander (=cilantro). Foci was first reported in California in 2005; a new and highly aggressive race 4 of Foa was observed in 2013 in California. Preliminary evidence indicated that Foa can also cause disease on coriander, albeit are less virulent than Foci. Comparative genomics was used to investigate the evolutionary relationships between Foa race 4, Foa race 3, and the Foci, which are all in FOSC Clade 2, and Foa race 2, which is in FOSC Clade 3.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">A phylogenetic analysis of 2718 single-copy conserved genes and mitochondrial DNA sequence indicated that Foa races 3 and 4 and the Foci are monophyletic within FOSC Clade 2; these strains also are in a single somatic compatibility group. However, in the accessory genomes, the Foci versus Foa races 3 and 4 differ in multiple contigs. Based on significantly increased expression of Foa race 4 genes in planta vs. in vitro, we identified 23 putative effectors and 13 possible pathogenicity factors. PCR primers for diagnosis of either Foa race 2 or 4 and the Foci were identified. Finally, mixtures of conidia that were pre-stained with different fluorochromes indicated that Foa race 4 formed conidial anastomosis tubes (CATs) with Foci. Foa race 4 and Foa race 2, which are in different somatic compatibility groups, did not form CATs with each other.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">There was no evidence that Foa race 2 was involved in the recent evolution of Foa race 4; Foa race 2 and 4 are CAT-incompatible. Although Foa races 3 and 4 and the Foci are closely related, there is no evidence that either Foci contributed to the evolution of Foa race 4, or that Foa race 4 was the recent recipient of a multi-gene chromosomal segment from another strain. However, horizontal chromosome transfer could account for the major difference in the accessory genomes of Foa race 4 and the Foci and for their differences in host range.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Henry</LastName><ForeName>Peter</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>USDA-ARS, 1636 East Alisal St., Salinas, CA, 93905, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kaur</LastName><ForeName>Sukhwinder</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pham</LastName><ForeName>Quyen Anh Tran</ForeName><Initials>QAT</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Current address: Janssen Biopharma, Inc., 260 E Grand Ave., South San Francisco, CA, 94080, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Barakat</LastName><ForeName>Radwan</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Plant Production & Protection, College of Agriculture, Hebron University, Hebron, Palestine.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Brinker</LastName><ForeName>Samuel</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Haensel</LastName><ForeName>Hannah</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Daugovish</LastName><ForeName>Oleg</ForeName><Initials>O</Initials><AffiliationInfo><Affiliation>University of California Cooperative Extension, 669 County Square Drive, Suite 100, Ventura, CA, 93003, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Epstein</LastName><ForeName>Lynn</ForeName><Initials>L</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-8697-1227</Identifier><AffiliationInfo><Affiliation>Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA. lepstein@ucdavis.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>10</Month><Day>20</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Apium graveolens</Keyword><Keyword MajorTopicYN="N">Celery</Keyword><Keyword MajorTopicYN="N">Cilantro</Keyword><Keyword MajorTopicYN="N">Coriander</Keyword><Keyword MajorTopicYN="N">Coriandrum sativum</Keyword><Keyword MajorTopicYN="N">Differentially expressed genes</Keyword><Keyword MajorTopicYN="N">Fusarium oxysporum</Keyword><Keyword MajorTopicYN="N">Fusarium oxysporum species complex</Keyword><Keyword MajorTopicYN="N">Fusarium yellows</Keyword><Keyword MajorTopicYN="N">Transposable elements</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>05</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>10</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>10</Month><Day>21</Day><Hour>5</Hour><Minute>37</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>10</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>10</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">33081696</ArticleId><ArticleId IdType="doi">10.1186/s12864-020-07141-5</ArticleId><ArticleId IdType="pii">10.1186/s12864-020-07141-5</ArticleId><ArticleId 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name="États-Unis"><noRegion><name sortKey="Henry, Peter" sort="Henry, Peter" uniqKey="Henry P" first="Peter" last="Henry">Peter Henry</name></noRegion><name sortKey="Barakat, Radwan" sort="Barakat, Radwan" uniqKey="Barakat R" first="Radwan" last="Barakat">Radwan Barakat</name><name sortKey="Brinker, Samuel" sort="Brinker, Samuel" uniqKey="Brinker S" first="Samuel" last="Brinker">Samuel Brinker</name><name sortKey="Daugovish, Oleg" sort="Daugovish, Oleg" uniqKey="Daugovish O" first="Oleg" last="Daugovish">Oleg Daugovish</name><name sortKey="Epstein, Lynn" sort="Epstein, Lynn" uniqKey="Epstein L" first="Lynn" last="Epstein">Lynn Epstein</name><name sortKey="Haensel, Hannah" sort="Haensel, Hannah" uniqKey="Haensel H" first="Hannah" last="Haensel">Hannah Haensel</name><name sortKey="Henry, Peter" sort="Henry, Peter" uniqKey="Henry P" first="Peter" last="Henry">Peter Henry</name><name sortKey="Kaur, Sukhwinder" sort="Kaur, Sukhwinder" uniqKey="Kaur S" first="Sukhwinder" last="Kaur">Sukhwinder Kaur</name><name sortKey="Pham, Quyen Anh Tran" sort="Pham, Quyen Anh Tran" uniqKey="Pham Q" first="Quyen Anh Tran" last="Pham">Quyen Anh Tran Pham</name><name sortKey="Pham, Quyen Anh Tran" sort="Pham, Quyen Anh Tran" uniqKey="Pham Q" first="Quyen Anh Tran" last="Pham">Quyen Anh Tran Pham</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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