Genomic Characterization of a South American Phytophthora Hybrid Mandates Reassessment of the Geographic Origins of Phytophthora infestans.
Identifieur interne : 000D26 ( Main/Corpus ); précédent : 000D25; suivant : 000D27Genomic Characterization of a South American Phytophthora Hybrid Mandates Reassessment of the Geographic Origins of Phytophthora infestans.
Auteurs : Michael D. Martin ; Filipe G. Vieira ; Simon Y W. Ho ; Nathan Wales ; Mikkel Schubert ; Andaine Seguin-Orlando ; Jean B. Ristaino ; M Thomas P. GilbertSource :
- Molecular biology and evolution [ 1537-1719 ] ; 2016.
English descriptors
- KwdEn :
- Evolution, Molecular (MeSH), Gene Flow (MeSH), Genome (MeSH), Genome, Mitochondrial (MeSH), Genomics (methods), Genotype (MeSH), Haplotypes (MeSH), Hybridization, Genetic (MeSH), Linkage Disequilibrium (MeSH), Phylogeny (MeSH), Phytophthora infestans (classification), Phytophthora infestans (genetics), Plant Diseases (MeSH), Reproduction (genetics), South America (MeSH).
- MESH :
- classification : Phytophthora infestans.
- genetics : Phytophthora infestans, Reproduction.
- methods : Genomics.
- Evolution, Molecular, Gene Flow, Genome, Genome, Mitochondrial, Genotype, Haplotypes, Hybridization, Genetic, Linkage Disequilibrium, Phylogeny, Plant Diseases, South America.
Abstract
As the oomycete pathogen causing potato late blight disease, Phytophthora infestans triggered the famous 19th-century Irish potato famine and remains the leading cause of global commercial potato crop destruction. But the geographic origin of the genotype that caused this devastating initial outbreak remains disputed, as does the New World center of origin of the species itself. Both Mexico and South America have been proposed, generating considerable controversy. Here, we readdress the pathogen's origins using a genomic data set encompassing 71 globally sourced modern and historical samples of P. infestans and the hybrid species P. andina, a close relative known only from the Andean highlands. Previous studies have suggested that the nuclear DNA lineage behind the initial outbreaks in Europe in 1845 is now extinct. Analysis of P. andina's phased haplotypes recovered eight haploid genome sequences, four of which represent a previously unknown basal lineage of P. infestans closely related to the famine-era lineage. Our analyses further reveal that clonal lineages of both P. andina and historical P. infestans diverged earlier than modern Mexican lineages, casting doubt on recent claims of a Mexican center of origin. Finally, we use haplotype phasing to demonstrate that basal branches of the clade comprising Mexican samples are occupied by clonal isolates collected from wild Solanum hosts, suggesting that modern Mexican P. infestans diversified on Solanum tuberosum after a host jump from a wild species and that the origins of P. infestans are more complex than was previously thought.
DOI: 10.1093/molbev/msv241
PubMed: 26576850
PubMed Central: PMC4866541
Links to Exploration step
pubmed:26576850Le document en format XML
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Martin</name><affiliation><nlm:affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark Department of Integrative Biology, Center for Theoretical Evolutionary Genomics, University of California, Berkeley sameoldmike@gmail.com.</nlm:affiliation></affiliation></author><author><name sortKey="Vieira, Filipe G" sort="Vieira, Filipe G" uniqKey="Vieira F" first="Filipe G" last="Vieira">Filipe G. Vieira</name><affiliation><nlm:affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.</nlm:affiliation></affiliation></author><author><name sortKey="Ho, Simon Y W" sort="Ho, Simon Y W" uniqKey="Ho S" first="Simon Y W" last="Ho">Simon Y W. Ho</name><affiliation><nlm:affiliation>School of Biological Sciences, University of Sydney, Sydney, NSW, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Wales, Nathan" sort="Wales, Nathan" uniqKey="Wales N" first="Nathan" last="Wales">Nathan Wales</name><affiliation><nlm:affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.</nlm:affiliation></affiliation></author><author><name sortKey="Schubert, Mikkel" sort="Schubert, Mikkel" uniqKey="Schubert M" first="Mikkel" last="Schubert">Mikkel Schubert</name><affiliation><nlm:affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.</nlm:affiliation></affiliation></author><author><name sortKey="Seguin Orlando, Andaine" sort="Seguin Orlando, Andaine" uniqKey="Seguin Orlando A" first="Andaine" last="Seguin-Orlando">Andaine Seguin-Orlando</name><affiliation><nlm:affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.</nlm:affiliation></affiliation></author><author><name sortKey="Ristaino, Jean B" sort="Ristaino, Jean B" uniqKey="Ristaino J" first="Jean B" last="Ristaino">Jean B. Ristaino</name><affiliation><nlm:affiliation>Department of Plant Pathology, North Carolina State University.</nlm:affiliation></affiliation></author><author><name sortKey="Gilbert, M Thomas P" sort="Gilbert, M Thomas P" uniqKey="Gilbert M" first="M Thomas P" last="Gilbert">M Thomas P. Gilbert</name><affiliation><nlm:affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Molecular biology and evolution</title><idno type="eISSN">1537-1719</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Evolution, Molecular (MeSH)</term><term>Gene Flow (MeSH)</term><term>Genome (MeSH)</term><term>Genome, Mitochondrial (MeSH)</term><term>Genomics (methods)</term><term>Genotype (MeSH)</term><term>Haplotypes (MeSH)</term><term>Hybridization, Genetic (MeSH)</term><term>Linkage Disequilibrium (MeSH)</term><term>Phylogeny (MeSH)</term><term>Phytophthora infestans (classification)</term><term>Phytophthora infestans (genetics)</term><term>Plant Diseases (MeSH)</term><term>Reproduction (genetics)</term><term>South America (MeSH)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Phytophthora infestans</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Phytophthora infestans</term><term>Reproduction</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Gene Flow</term><term>Genome</term><term>Genome, Mitochondrial</term><term>Genotype</term><term>Haplotypes</term><term>Hybridization, Genetic</term><term>Linkage Disequilibrium</term><term>Phylogeny</term><term>Plant Diseases</term><term>South America</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">As the oomycete pathogen causing potato late blight disease, Phytophthora infestans triggered the famous 19th-century Irish potato famine and remains the leading cause of global commercial potato crop destruction. But the geographic origin of the genotype that caused this devastating initial outbreak remains disputed, as does the New World center of origin of the species itself. Both Mexico and South America have been proposed, generating considerable controversy. Here, we readdress the pathogen's origins using a genomic data set encompassing 71 globally sourced modern and historical samples of P. infestans and the hybrid species P. andina, a close relative known only from the Andean highlands. Previous studies have suggested that the nuclear DNA lineage behind the initial outbreaks in Europe in 1845 is now extinct. Analysis of P. andina's phased haplotypes recovered eight haploid genome sequences, four of which represent a previously unknown basal lineage of P. infestans closely related to the famine-era lineage. Our analyses further reveal that clonal lineages of both P. andina and historical P. infestans diverged earlier than modern Mexican lineages, casting doubt on recent claims of a Mexican center of origin. Finally, we use haplotype phasing to demonstrate that basal branches of the clade comprising Mexican samples are occupied by clonal isolates collected from wild Solanum hosts, suggesting that modern Mexican P. infestans diversified on Solanum tuberosum after a host jump from a wild species and that the origins of P. infestans are more complex than was previously thought. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26576850</PMID><DateCompleted><Year>2016</Year><Month>10</Month><Day>20</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1537-1719</ISSN><JournalIssue CitedMedium="Internet"><Volume>33</Volume><Issue>2</Issue><PubDate><Year>2016</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Molecular biology and evolution</Title><ISOAbbreviation>Mol Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Genomic Characterization of a South American Phytophthora Hybrid Mandates Reassessment of the Geographic Origins of Phytophthora infestans.</ArticleTitle><Pagination><MedlinePgn>478-91</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/molbev/msv241</ELocationID><Abstract><AbstractText>As the oomycete pathogen causing potato late blight disease, Phytophthora infestans triggered the famous 19th-century Irish potato famine and remains the leading cause of global commercial potato crop destruction. But the geographic origin of the genotype that caused this devastating initial outbreak remains disputed, as does the New World center of origin of the species itself. Both Mexico and South America have been proposed, generating considerable controversy. Here, we readdress the pathogen's origins using a genomic data set encompassing 71 globally sourced modern and historical samples of P. infestans and the hybrid species P. andina, a close relative known only from the Andean highlands. Previous studies have suggested that the nuclear DNA lineage behind the initial outbreaks in Europe in 1845 is now extinct. Analysis of P. andina's phased haplotypes recovered eight haploid genome sequences, four of which represent a previously unknown basal lineage of P. infestans closely related to the famine-era lineage. Our analyses further reveal that clonal lineages of both P. andina and historical P. infestans diverged earlier than modern Mexican lineages, casting doubt on recent claims of a Mexican center of origin. Finally, we use haplotype phasing to demonstrate that basal branches of the clade comprising Mexican samples are occupied by clonal isolates collected from wild Solanum hosts, suggesting that modern Mexican P. infestans diversified on Solanum tuberosum after a host jump from a wild species and that the origins of P. infestans are more complex than was previously thought. </AbstractText><CopyrightInformation>© The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Martin</LastName><ForeName>Michael D</ForeName><Initials>MD</Initials><AffiliationInfo><Affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark Department of Integrative Biology, Center for Theoretical Evolutionary Genomics, University of California, Berkeley sameoldmike@gmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vieira</LastName><ForeName>Filipe G</ForeName><Initials>FG</Initials><AffiliationInfo><Affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ho</LastName><ForeName>Simon Y W</ForeName><Initials>SY</Initials><AffiliationInfo><Affiliation>School of Biological Sciences, University of Sydney, Sydney, NSW, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wales</LastName><ForeName>Nathan</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schubert</LastName><ForeName>Mikkel</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Seguin-Orlando</LastName><ForeName>Andaine</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ristaino</LastName><ForeName>Jean B</ForeName><Initials>JB</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, North Carolina State University.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gilbert</LastName><ForeName>M Thomas P</ForeName><Initials>MT</Initials><AffiliationInfo><Affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia.</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>2015</Year><Month>11</Month><Day>17</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Biol Evol</MedlineTA><NlmUniqueID>8501455</NlmUniqueID><ISSNLinking>0737-4038</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D051456" MajorTopicYN="N">Gene Flow</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016678" MajorTopicYN="Y">Genome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054629" MajorTopicYN="N">Genome, Mitochondrial</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="Y">Genomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006239" MajorTopicYN="N">Haplotypes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006824" MajorTopicYN="Y">Hybridization, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015810" MajorTopicYN="N">Linkage Disequilibrium</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055750" MajorTopicYN="N">Phytophthora infestans</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012098" MajorTopicYN="N">Reproduction</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013020" MajorTopicYN="N">South America</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Phytophthora andina</Keyword><Keyword MajorTopicYN="N">Phytophthora infestans</Keyword><Keyword MajorTopicYN="N">pathogen</Keyword><Keyword MajorTopicYN="N">phylogenomics</Keyword><Keyword MajorTopicYN="N">plant disease</Keyword><Keyword MajorTopicYN="N">population genomics</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>11</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>11</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>10</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26576850</ArticleId><ArticleId IdType="pii">msv241</ArticleId><ArticleId IdType="doi">10.1093/molbev/msv241</ArticleId><ArticleId 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