Population genomics of an outbreak of the potato late blight pathogen, Phytophthora infestans, reveals both clonality and high genotypic diversity.
Identifieur interne : 000412 ( Main/Exploration ); précédent : 000411; suivant : 000413Population genomics of an outbreak of the potato late blight pathogen, Phytophthora infestans, reveals both clonality and high genotypic diversity.
Auteurs : Sundy Maurice [Norvège] ; Melanie S. Montes [Danemark] ; Bent J. Nielsen [Danemark] ; Lars B Dker [Danemark] ; Michael D. Martin [Danemark] ; Carina G. J Nck [Danemark] ; Rasmus Kj Ller [Danemark] ; S Ren Rosendahl [Danemark]Source :
- Molecular plant pathology [ 1364-3703 ] ; 2019.
Descripteurs français
- KwdFr :
- Clones cellulaires (MeSH), Danemark (MeSH), Génomique (MeSH), Génotype (MeSH), Géographie (MeSH), Maladies des plantes (microbiologie), Phytophthora infestans (génétique), Ploïdies (MeSH), Polymorphisme de nucléotide simple (génétique), Recombinaison génétique (génétique), Répétitions microsatellites (génétique), Solanum tuberosum (microbiologie), Variation génétique (MeSH), Épidémies de maladies (MeSH).
- MESH :
- Wicri :
- geographic : Danemark.
English descriptors
- KwdEn :
- Clone Cells (MeSH), Denmark (MeSH), Disease Outbreaks (MeSH), Genetic Variation (MeSH), Genomics (MeSH), Genotype (MeSH), Geography (MeSH), Microsatellite Repeats (genetics), Phytophthora infestans (genetics), Plant Diseases (microbiology), Ploidies (MeSH), Polymorphism, Single Nucleotide (genetics), Recombination, Genetic (genetics), Solanum tuberosum (microbiology).
- MESH :
- geographic : Denmark.
- genetics : Microsatellite Repeats, Phytophthora infestans, Polymorphism, Single Nucleotide, Recombination, Genetic.
- microbiology : Plant Diseases, Solanum tuberosum.
- Clone Cells, Disease Outbreaks, Genetic Variation, Genomics, Genotype, Geography, Ploidies.
Abstract
An outbreak of the potato late blight pathogen Phytophthora infestans in Denmark was characterized in order to resolve the population structure and determine to what extent sexual reproduction was occurring. A standard set of microsatellite simple sequence repeats (SSRs) and single nucleotide polymorphism (SNP) markers generated using restriction site-associated DNA sequencing (RAD-seq) were employed in parallel. A total of 83 individuals, isolated from seven different potato fields in 2014, were analysed together with five Danish whole-genome sequenced isolates, as well as two Mexican individuals used as an outgroup. From a filtered dataset of 55 288 SNPs, population genomics analyses revealed no sign of recombination, implying clonality. In spite of this, multilocus genotypes were unique to individual potato fields, with little evidence of gene flow between fields. Ploidy analysis performed on the SNPs dataset indicated that the majority of isolates were diploid. These contradictory results with clonality and high genotypic diversity may suggest that rare sexual events likely still contribute to the population. Comparison of the results generated by SSRs vs SNPs data indicated that large marker sets, generated by RAD-seq, may be advised going forward, as it provides a higher level of genetic discrimination than SSRs.
DOI: 10.1111/mpp.12819
PubMed: 31145530
PubMed Central: PMC6640178
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Montes</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen O, 2100, Denmark.</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen O, 2100</wicri:regionArea><wicri:noRegion>2100</wicri:noRegion></affiliation></author><author><name sortKey="Nielsen, Bent J" sort="Nielsen, Bent J" uniqKey="Nielsen B" first="Bent J" last="Nielsen">Bent J. Nielsen</name><affiliation wicri:level="1"><nlm:affiliation>Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, 4200, Denmark.</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, 4200</wicri:regionArea><wicri:noRegion>4200</wicri:noRegion></affiliation></author><author><name sortKey="B Dker, Lars" sort="B Dker, Lars" uniqKey="B Dker L" first="Lars" last="B Dker">Lars B Dker</name><affiliation wicri:level="1"><nlm:affiliation>Danish Centre for Food and Agriculture, Aarhus University, Blichers Allé 20, Tjele, 8830, Denmark.</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Danish Centre for Food and Agriculture, Aarhus University, Blichers Allé 20, Tjele, 8830</wicri:regionArea><wicri:noRegion>8830</wicri:noRegion></affiliation></author><author><name sortKey="Martin, Michael D" sort="Martin, Michael D" uniqKey="Martin M" first="Michael D" last="Martin">Michael D. Martin</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Geogenetics, Natural History Museum of Denmark, Sølvgade 83, Copenhagen-K, 1307, Denmark.</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Centre for Geogenetics, Natural History Museum of Denmark, Sølvgade 83, Copenhagen-K, 1307</wicri:regionArea><wicri:noRegion>1307</wicri:noRegion></affiliation></author><author><name sortKey="J Nck, Carina G" sort="J Nck, Carina G" uniqKey="J Nck C" first="Carina G" last="J Nck">Carina G. J Nck</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen O, 2100, Denmark.</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen O, 2100</wicri:regionArea><wicri:noRegion>2100</wicri:noRegion></affiliation></author><author><name sortKey="Kj Ller, Rasmus" sort="Kj Ller, Rasmus" uniqKey="Kj Ller R" first="Rasmus" last="Kj Ller">Rasmus Kj Ller</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen O, 2100, Denmark.</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen O, 2100</wicri:regionArea><wicri:noRegion>2100</wicri:noRegion></affiliation></author><author><name sortKey="Rosendahl, S Ren" sort="Rosendahl, S Ren" uniqKey="Rosendahl S" first="S Ren" last="Rosendahl">S Ren Rosendahl</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen O, 2100, Denmark.</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen O, 2100</wicri:regionArea><wicri:noRegion>2100</wicri:noRegion></affiliation></author></analytic><series><title level="j">Molecular plant pathology</title><idno type="eISSN">1364-3703</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Clone Cells (MeSH)</term><term>Denmark (MeSH)</term><term>Disease Outbreaks (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genomics (MeSH)</term><term>Genotype (MeSH)</term><term>Geography (MeSH)</term><term>Microsatellite Repeats (genetics)</term><term>Phytophthora infestans (genetics)</term><term>Plant Diseases (microbiology)</term><term>Ploidies (MeSH)</term><term>Polymorphism, Single Nucleotide (genetics)</term><term>Recombination, Genetic (genetics)</term><term>Solanum tuberosum (microbiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Clones cellulaires (MeSH)</term><term>Danemark (MeSH)</term><term>Génomique (MeSH)</term><term>Génotype (MeSH)</term><term>Géographie (MeSH)</term><term>Maladies des plantes (microbiologie)</term><term>Phytophthora infestans (génétique)</term><term>Ploïdies (MeSH)</term><term>Polymorphisme de nucléotide simple (génétique)</term><term>Recombinaison génétique (génétique)</term><term>Répétitions microsatellites (génétique)</term><term>Solanum tuberosum (microbiologie)</term><term>Variation génétique (MeSH)</term><term>Épidémies de maladies (MeSH)</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Denmark</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Microsatellite Repeats</term><term>Phytophthora infestans</term><term>Polymorphism, Single Nucleotide</term><term>Recombination, Genetic</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Phytophthora infestans</term><term>Polymorphisme de nucléotide simple</term><term>Recombinaison génétique</term><term>Répétitions microsatellites</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Maladies des plantes</term><term>Solanum tuberosum</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Diseases</term><term>Solanum tuberosum</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Clone Cells</term><term>Disease Outbreaks</term><term>Genetic Variation</term><term>Genomics</term><term>Genotype</term><term>Geography</term><term>Ploidies</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Clones cellulaires</term><term>Danemark</term><term>Génomique</term><term>Génotype</term><term>Géographie</term><term>Ploïdies</term><term>Variation génétique</term><term>Épidémies de maladies</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Danemark</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">An outbreak of the potato late blight pathogen Phytophthora infestans in Denmark was characterized in order to resolve the population structure and determine to what extent sexual reproduction was occurring. A standard set of microsatellite simple sequence repeats (SSRs) and single nucleotide polymorphism (SNP) markers generated using restriction site-associated DNA sequencing (RAD-seq) were employed in parallel. A total of 83 individuals, isolated from seven different potato fields in 2014, were analysed together with five Danish whole-genome sequenced isolates, as well as two Mexican individuals used as an outgroup. From a filtered dataset of 55 288 SNPs, population genomics analyses revealed no sign of recombination, implying clonality. In spite of this, multilocus genotypes were unique to individual potato fields, with little evidence of gene flow between fields. Ploidy analysis performed on the SNPs dataset indicated that the majority of isolates were diploid. These contradictory results with clonality and high genotypic diversity may suggest that rare sexual events likely still contribute to the population. Comparison of the results generated by SSRs vs SNPs data indicated that large marker sets, generated by RAD-seq, may be advised going forward, as it provides a higher level of genetic discrimination than SSRs.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31145530</PMID><DateCompleted><Year>2020</Year><Month>06</Month><Day>19</Day></DateCompleted><DateRevised><Year>2020</Year><Month>06</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1364-3703</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>8</Issue><PubDate><Year>2019</Year><Month>08</Month></PubDate></JournalIssue><Title>Molecular plant pathology</Title><ISOAbbreviation>Mol Plant Pathol</ISOAbbreviation></Journal><ArticleTitle>Population genomics of an outbreak of the potato late blight pathogen, Phytophthora infestans, reveals both clonality and high genotypic diversity.</ArticleTitle><Pagination><MedlinePgn>1134-1146</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/mpp.12819</ELocationID><Abstract><AbstractText>An outbreak of the potato late blight pathogen Phytophthora infestans in Denmark was characterized in order to resolve the population structure and determine to what extent sexual reproduction was occurring. A standard set of microsatellite simple sequence repeats (SSRs) and single nucleotide polymorphism (SNP) markers generated using restriction site-associated DNA sequencing (RAD-seq) were employed in parallel. A total of 83 individuals, isolated from seven different potato fields in 2014, were analysed together with five Danish whole-genome sequenced isolates, as well as two Mexican individuals used as an outgroup. From a filtered dataset of 55 288 SNPs, population genomics analyses revealed no sign of recombination, implying clonality. In spite of this, multilocus genotypes were unique to individual potato fields, with little evidence of gene flow between fields. Ploidy analysis performed on the SNPs dataset indicated that the majority of isolates were diploid. These contradictory results with clonality and high genotypic diversity may suggest that rare sexual events likely still contribute to the population. Comparison of the results generated by SSRs vs SNPs data indicated that large marker sets, generated by RAD-seq, may be advised going forward, as it provides a higher level of genetic discrimination than SSRs.</AbstractText><CopyrightInformation>© 2019 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>Maurice</LastName><ForeName>Sundy</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Blindernveien 31, Oslo, 0316, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Montes</LastName><ForeName>Melanie S</ForeName><Initials>MS</Initials><Identifier Source="ORCID">0000-0001-9034-7259</Identifier><AffiliationInfo><Affiliation>Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen O, 2100, Denmark.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nielsen</LastName><ForeName>Bent J</ForeName><Initials>BJ</Initials><AffiliationInfo><Affiliation>Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, 4200, Denmark.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bødker</LastName><ForeName>Lars</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Danish Centre for Food and Agriculture, Aarhus University, Blichers Allé 20, Tjele, 8830, Denmark.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Martin</LastName><ForeName>Michael D</ForeName><Initials>MD</Initials><AffiliationInfo><Affiliation>Centre for Geogenetics, Natural History Museum of Denmark, Sølvgade 83, Copenhagen-K, 1307, Denmark.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jønck</LastName><ForeName>Carina G</ForeName><Initials>CG</Initials><AffiliationInfo><Affiliation>Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen O, 2100, Denmark.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kjøller</LastName><ForeName>Rasmus</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen O, 2100, Denmark.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rosendahl</LastName><ForeName>Søren</ForeName><Initials>S</Initials><Identifier Source="ORCID">0000-0001-5202-6585</Identifier><AffiliationInfo><Affiliation>Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen O, 2100, Denmark.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>05</Month><Day>30</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Plant Pathol</MedlineTA><NlmUniqueID>100954969</NlmUniqueID><ISSNLinking>1364-3703</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002999" MajorTopicYN="N">Clone Cells</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003718" MajorTopicYN="N" Type="Geographic">Denmark</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004196" MajorTopicYN="Y">Disease Outbreaks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="Y">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005843" MajorTopicYN="N">Geography</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="N">Microsatellite Repeats</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D055750" MajorTopicYN="N">Phytophthora infestans</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011003" MajorTopicYN="N">Ploidies</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011995" MajorTopicYN="N">Recombination, Genetic</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011198" MajorTopicYN="N">Solanum tuberosum</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Phytophthora infestans
</Keyword><Keyword MajorTopicYN="Y">RAD sequencing</Keyword><Keyword MajorTopicYN="Y">SNPs</Keyword><Keyword MajorTopicYN="Y">clonality</Keyword><Keyword MajorTopicYN="Y">plant pathogen</Keyword><Keyword MajorTopicYN="Y">ploidy</Keyword><Keyword MajorTopicYN="Y">population structure</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>5</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>6</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>5</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31145530</ArticleId><ArticleId IdType="doi">10.1111/mpp.12819</ArticleId><ArticleId 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IdType="pubmed">30708842</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Danemark</li><li>Norvège</li></country></list><tree><country name="Norvège"><noRegion><name sortKey="Maurice, Sundy" sort="Maurice, Sundy" uniqKey="Maurice S" first="Sundy" last="Maurice">Sundy Maurice</name></noRegion></country><country name="Danemark"><noRegion><name sortKey="Montes, Melanie S" sort="Montes, Melanie S" uniqKey="Montes M" first="Melanie S" last="Montes">Melanie S. Montes</name></noRegion><name sortKey="B Dker, Lars" sort="B Dker, Lars" uniqKey="B Dker L" first="Lars" last="B Dker">Lars B Dker</name><name sortKey="J Nck, Carina G" sort="J Nck, Carina G" uniqKey="J Nck C" first="Carina G" last="J Nck">Carina G. J Nck</name><name sortKey="Kj Ller, Rasmus" sort="Kj Ller, Rasmus" uniqKey="Kj Ller R" first="Rasmus" last="Kj Ller">Rasmus Kj Ller</name><name sortKey="Martin, Michael D" sort="Martin, Michael D" uniqKey="Martin M" first="Michael D" last="Martin">Michael D. Martin</name><name sortKey="Nielsen, Bent J" sort="Nielsen, Bent J" uniqKey="Nielsen B" first="Bent J" last="Nielsen">Bent J. Nielsen</name><name sortKey="Rosendahl, S Ren" sort="Rosendahl, S Ren" uniqKey="Rosendahl S" first="S Ren" last="Rosendahl">S Ren Rosendahl</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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