Molecular phylogenomics and population structure of Phytophthora pluvialis.
Identifieur interne : 000115 ( Main/Exploration ); précédent : 000114; suivant : 000116Molecular phylogenomics and population structure of Phytophthora pluvialis.
Auteurs : Javier Tabima [États-Unis] ; Lilah Gonen [États-Unis] ; Mireia G Mez-Gallego [France] ; Preeti Panda [Nouvelle-Zélande] ; Niklaus J. Grünwald [États-Unis] ; Rebecca Mcdougal [Oman] ; Everett Hansen [États-Unis] ; Jared Leboldus [États-Unis] ; Nari M. Williams [Nouvelle-Zélande]Source :
- Phytopathology [ 0031-949X ] ; 2020.
Abstract
Phytophthora pluvialis is an oomycete that was first isolated from soil, water, and tree foliage in mixed Douglas-fir - tanoak forests of the US Pacific Northwest (PNW). It was then identified as the causal agent of red needle cast (RNC) of radiata pine (Pinus radiata) in New Zealand (NZ). Genotyping-by-sequencing (GBS) was used to obtain 1,543 single nucleotide polymorphisms (SNPs) across 145 P. pluvialis isolates to characterize the population structure in the PNW and NZ. We tested the hypothesis that P. pluvialis was introduced to NZ from the PNW using genetic distance measurements and population structure analyzes among locations between countries, . The low genetic distance, population heterozygosity, and lack of geographic structure in NZ, suggest a single colonization event from the US followed by clonal expansion in NZ. The PNW Coast Range was proposed as a presumptive center of origin of the currently known distribution of P. pluvialis based on its geographic range and position as the central cluster in a minimum spanning network. The Coastal cluster of isolates were located at the root of every US cluster, and emerged earlier than all NZ clusters. The Coastal cluster had the highest degree of heterozygosity (Hs = 0.254) and median pairwise genetic distance (0.093) relative to any other cluster. Finally, the rapid host diversification between closely related isolates of P. pluvialis in New Zealand, indicate that this pathogen has the potential to infect a broader range of hosts than is currently recognized.
DOI: 10.1094/PHYTO-06-20-0232-FI
PubMed: 33048632
Affiliations:
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Grünwald</name><affiliation wicri:level="1"><nlm:affiliation>USDA ARS, Horticultural Crops Research Laboratory, 3420 NW Orchard Ave, Corvallis, Oregon, United States, 97330; grunwaln@oregonstate.edu.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>USDA ARS, Horticultural Crops Research Laboratory, 3420 NW Orchard Ave, Corvallis, Oregon, United States</wicri:regionArea><wicri:noRegion>United States</wicri:noRegion></affiliation></author><author><name sortKey="Mcdougal, Rebecca" sort="Mcdougal, Rebecca" uniqKey="Mcdougal R" first="Rebecca" last="Mcdougal">Rebecca Mcdougal</name><affiliation wicri:level="1"><nlm:affiliation>New Zealand Forest Research Institute, 6982, Rotorua, New Zealand; Rebecca.McDougal@scionresearch.com.</nlm:affiliation><country wicri:rule="url">Oman</country><wicri:regionArea>New Zealand Forest Research Institute, 6982, Rotorua</wicri:regionArea><wicri:noRegion>Rotorua</wicri:noRegion></affiliation></author><author><name sortKey="Hansen, Everett" sort="Hansen, Everett" uniqKey="Hansen E" first="Everett" last="Hansen">Everett Hansen</name><affiliation wicri:level="1"><nlm:affiliation>Oregon State Univ., Botany and Plant Pathology, Cordley Hall, Corvallis, Oregon, United States, 97331; hansene@science.oregonstate.edu.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Oregon State Univ., Botany and Plant Pathology, Cordley Hall, Corvallis, Oregon, United States</wicri:regionArea><wicri:noRegion>United States</wicri:noRegion></affiliation></author><author><name sortKey="Leboldus, Jared" sort="Leboldus, Jared" uniqKey="Leboldus J" first="Jared" last="Leboldus">Jared Leboldus</name><affiliation wicri:level="1"><nlm:affiliation>2062 Cordely HallCorvallis, Oregon, United States, 97331; jared.leboldus@science.oregonstate.edu.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>2062 Cordely HallCorvallis, Oregon, United States</wicri:regionArea><wicri:noRegion>United States</wicri:noRegion></affiliation></author><author><name sortKey="Williams, Nari M" sort="Williams, Nari M" uniqKey="Williams N" first="Nari M" last="Williams">Nari M. Williams</name><affiliation wicri:level="1"><nlm:affiliation>New Zealand Institute for Plant and Food Research Ltd, 1413, Pathology, Cnr Crosses and St George's Roads, Havelock North, Auckland, Hawkes Bay, New Zealand, 1142; nari.williams@plantandfood.co.nz.</nlm:affiliation><country wicri:rule="url">Nouvelle-Zélande</country><wicri:regionArea>New Zealand Institute for Plant and Food Research Ltd, 1413, Pathology, Cnr Crosses and St George's Roads, Havelock North, Auckland, Hawkes Bay, New Zealand</wicri:regionArea><wicri:noRegion>New Zealand</wicri:noRegion></affiliation></author></analytic><series><title level="j">Phytopathology</title><idno type="ISSN">0031-949X</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">Phytophthora pluvialis is an oomycete that was first isolated from soil, water, and tree foliage in mixed Douglas-fir - tanoak forests of the US Pacific Northwest (PNW). It was then identified as the causal agent of red needle cast (RNC) of radiata pine (Pinus radiata) in New Zealand (NZ). Genotyping-by-sequencing (GBS) was used to obtain 1,543 single nucleotide polymorphisms (SNPs) across 145 P. pluvialis isolates to characterize the population structure in the PNW and NZ. We tested the hypothesis that P. pluvialis was introduced to NZ from the PNW using genetic distance measurements and population structure analyzes among locations between countries, . The low genetic distance, population heterozygosity, and lack of geographic structure in NZ, suggest a single colonization event from the US followed by clonal expansion in NZ. The PNW Coast Range was proposed as a presumptive center of origin of the currently known distribution of P. pluvialis based on its geographic range and position as the central cluster in a minimum spanning network. The Coastal cluster of isolates were located at the root of every US cluster, and emerged earlier than all NZ clusters. The Coastal cluster had the highest degree of heterozygosity (Hs = 0.254) and median pairwise genetic distance (0.093) relative to any other cluster. Finally, the rapid host diversification between closely related isolates of P. pluvialis in New Zealand, indicate that this pathogen has the potential to infect a broader range of hosts than is currently recognized.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">33048632</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0031-949X</ISSN><JournalIssue CitedMedium="Print"><PubDate><Year>2020</Year><Month>Oct</Month><Day>13</Day></PubDate></JournalIssue><Title>Phytopathology</Title><ISOAbbreviation>Phytopathology</ISOAbbreviation></Journal><ArticleTitle>Molecular phylogenomics and population structure of Phytophthora pluvialis.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1094/PHYTO-06-20-0232-FI</ELocationID><Abstract><AbstractText>Phytophthora pluvialis is an oomycete that was first isolated from soil, water, and tree foliage in mixed Douglas-fir - tanoak forests of the US Pacific Northwest (PNW). It was then identified as the causal agent of red needle cast (RNC) of radiata pine (Pinus radiata) in New Zealand (NZ). Genotyping-by-sequencing (GBS) was used to obtain 1,543 single nucleotide polymorphisms (SNPs) across 145 P. pluvialis isolates to characterize the population structure in the PNW and NZ. We tested the hypothesis that P. pluvialis was introduced to NZ from the PNW using genetic distance measurements and population structure analyzes among locations between countries, . The low genetic distance, population heterozygosity, and lack of geographic structure in NZ, suggest a single colonization event from the US followed by clonal expansion in NZ. The PNW Coast Range was proposed as a presumptive center of origin of the currently known distribution of P. pluvialis based on its geographic range and position as the central cluster in a minimum spanning network. The Coastal cluster of isolates were located at the root of every US cluster, and emerged earlier than all NZ clusters. The Coastal cluster had the highest degree of heterozygosity (Hs = 0.254) and median pairwise genetic distance (0.093) relative to any other cluster. Finally, the rapid host diversification between closely related isolates of P. pluvialis in New Zealand, indicate that this pathogen has the potential to infect a broader range of hosts than is currently recognized.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tabima</LastName><ForeName>Javier</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Oregon State University, 2694, Botany and Plant Pathology, Cordley Hall, Corvallis, Oregon, United States, 97331-4501; jtabima@clarku.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gonen</LastName><ForeName>Lilah</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Oregon State University, 2694, Botany and Plant Pathology, Corvallis, Oregon, United States; gonenl@oregonstate.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gómez-Gallego</LastName><ForeName>Mireia</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Scion, 6982, Forest Protection, 49 Sala Street, Private Bag 3020, Rotorua 3046, Rotorua, Bay of Plenty, New Zealand, 3010; mireia.gomez-gallego@inrae.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Panda</LastName><ForeName>Preeti</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Plant and Food Research Ltd, 1413, Havelock, New Zealand; Preeti.Panda@plantandfood.co.nz.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grünwald</LastName><ForeName>Niklaus J</ForeName><Initials>NJ</Initials><AffiliationInfo><Affiliation>USDA ARS, Horticultural Crops Research Laboratory, 3420 NW Orchard Ave, Corvallis, Oregon, United States, 97330; grunwaln@oregonstate.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>McDougal</LastName><ForeName>Rebecca</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>New Zealand Forest Research Institute, 6982, Rotorua, New Zealand; Rebecca.McDougal@scionresearch.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hansen</LastName><ForeName>Everett</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Oregon State Univ., Botany and Plant Pathology, Cordley Hall, Corvallis, Oregon, United States, 97331; hansene@science.oregonstate.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Leboldus</LastName><ForeName>Jared</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>2062 Cordely HallCorvallis, Oregon, United States, 97331; jared.leboldus@science.oregonstate.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Williams</LastName><ForeName>Nari M</ForeName><Initials>NM</Initials><AffiliationInfo><Affiliation>New Zealand Institute for Plant and Food Research Ltd, 1413, Pathology, Cnr Crosses and St George's Roads, Havelock North, Auckland, Hawkes Bay, New Zealand, 1142; nari.williams@plantandfood.co.nz.</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>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Phytopathology</MedlineTA><NlmUniqueID>9427222</NlmUniqueID><ISSNLinking>0031-949X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Diseases in Natural Plant Populations</Keyword><Keyword MajorTopicYN="N">Ecology</Keyword><Keyword MajorTopicYN="N">Forest Pathology</Keyword><Keyword MajorTopicYN="N">Genomics</Keyword><Keyword MajorTopicYN="N">Microbe-genome Sequencing</Keyword><Keyword MajorTopicYN="N">Oomycetes</Keyword><Keyword MajorTopicYN="N">Population Biology</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>10</Month><Day>13</Day><Hour>17</Hour><Minute>10</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>10</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>10</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">33048632</ArticleId><ArticleId IdType="doi">10.1094/PHYTO-06-20-0232-FI</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li><li>Nouvelle-Zélande</li><li>Oman</li><li>États-Unis</li></country><region><li>Oregon</li></region></list><tree><country name="États-Unis"><noRegion><name sortKey="Tabima, Javier" sort="Tabima, Javier" uniqKey="Tabima J" first="Javier" last="Tabima">Javier Tabima</name></noRegion><name sortKey="Gonen, Lilah" sort="Gonen, Lilah" uniqKey="Gonen L" first="Lilah" last="Gonen">Lilah Gonen</name><name sortKey="Grunwald, Niklaus J" sort="Grunwald, Niklaus J" uniqKey="Grunwald N" first="Niklaus J" last="Grünwald">Niklaus J. 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