Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes.
Identifieur interne : 000E82 ( Main/Corpus ); précédent : 000E81; suivant : 000E83Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes.
Auteurs : Sara Branco ; Ke Bi ; Hui-Ling Liao ; Pierre Gladieux ; Hélène Badouin ; Christopher E. Ellison ; Nhu H. Nguyen ; Rytas Vilgalys ; Kabir G. Peay ; John W. Taylor ; Thomas D. BrunsSource :
- Molecular ecology [ 1365-294X ] ; 2017.
English descriptors
- KwdEn :
- Adaptation, Physiological (genetics), Agaricales (genetics), Basidiomycota (genetics), Canada (MeSH), Climate (MeSH), Cold-Shock Response (genetics), DNA, Fungal (genetics), Genetics, Population (MeSH), Genome, Fungal (MeSH), Genotype (MeSH), Linkage Disequilibrium (MeSH), Mycorrhizae (genetics), North America (MeSH), Pinus (microbiology), Rain (MeSH), Selection, Genetic (MeSH), Snow (MeSH), Temperature (MeSH).
- MESH :
- chemical , genetics : DNA, Fungal.
- genetics : Adaptation, Physiological, Agaricales, Basidiomycota, Cold-Shock Response, Mycorrhizae.
- microbiology : Pinus.
- Canada, Climate, Genetics, Population, Genome, Fungal, Genotype, Linkage Disequilibrium, North America, Rain, Selection, Genetic, Snow, Temperature.
Abstract
Recent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with the roots of pine trees. We used genomic data from 55 individuals in seven locations across North America to perform genome scans to detect signatures of positive selection and assess whether temperature and precipitation were associated with genetic differentiation. We found that S. brevipes exhibited overall strong population differentiation, with potential admixture in Canadian populations. This species also displayed genomic signatures of positive selection as well as genomic sites significantly associated with distinct climatic regimes and abiotic environmental parameters. These genomic regions included genes involved in transmembrane transport of substances and helicase activity potentially involved in cold stress response. Our study sheds light on large-scale environmental adaptation in fungi by identifying putative adaptive genes and providing a framework to further investigate the genetic basis of fungal adaptation.
DOI: 10.1111/mec.13892
PubMed: 27761941
PubMed Central: PMC5392165
Links to Exploration step
pubmed:27761941Le document en format XML
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Nguyen</name><affiliation><nlm:affiliation>Department of Tropical Plant and Soil Sciences, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Vilgalys, Rytas" sort="Vilgalys, Rytas" uniqKey="Vilgalys R" first="Rytas" last="Vilgalys">Rytas Vilgalys</name><affiliation><nlm:affiliation>Department of Biology, Duke University, Durham, NC, 27708, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Peay, Kabir G" sort="Peay, Kabir G" uniqKey="Peay K" first="Kabir G" last="Peay">Kabir G. Peay</name><affiliation><nlm:affiliation>Department of Biology, Stanford University, Stanford, CA, 94305, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Taylor, John W" sort="Taylor, John W" uniqKey="Taylor J" first="John W" last="Taylor">John W. Taylor</name><affiliation><nlm:affiliation>Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bruns, Thomas D" sort="Bruns, Thomas D" uniqKey="Bruns T" first="Thomas D" last="Bruns">Thomas D. Bruns</name><affiliation><nlm:affiliation>Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720, USA.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Molecular ecology</title><idno type="eISSN">1365-294X</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adaptation, Physiological (genetics)</term><term>Agaricales (genetics)</term><term>Basidiomycota (genetics)</term><term>Canada (MeSH)</term><term>Climate (MeSH)</term><term>Cold-Shock Response (genetics)</term><term>DNA, Fungal (genetics)</term><term>Genetics, Population (MeSH)</term><term>Genome, Fungal (MeSH)</term><term>Genotype (MeSH)</term><term>Linkage Disequilibrium (MeSH)</term><term>Mycorrhizae (genetics)</term><term>North America (MeSH)</term><term>Pinus (microbiology)</term><term>Rain (MeSH)</term><term>Selection, Genetic (MeSH)</term><term>Snow (MeSH)</term><term>Temperature (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Fungal</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Adaptation, Physiological</term><term>Agaricales</term><term>Basidiomycota</term><term>Cold-Shock Response</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Pinus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Canada</term><term>Climate</term><term>Genetics, Population</term><term>Genome, Fungal</term><term>Genotype</term><term>Linkage Disequilibrium</term><term>North America</term><term>Rain</term><term>Selection, Genetic</term><term>Snow</term><term>Temperature</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Recent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with the roots of pine trees. We used genomic data from 55 individuals in seven locations across North America to perform genome scans to detect signatures of positive selection and assess whether temperature and precipitation were associated with genetic differentiation. We found that S. brevipes exhibited overall strong population differentiation, with potential admixture in Canadian populations. This species also displayed genomic signatures of positive selection as well as genomic sites significantly associated with distinct climatic regimes and abiotic environmental parameters. These genomic regions included genes involved in transmembrane transport of substances and helicase activity potentially involved in cold stress response. Our study sheds light on large-scale environmental adaptation in fungi by identifying putative adaptive genes and providing a framework to further investigate the genetic basis of fungal adaptation.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27761941</PMID><DateCompleted><Year>2017</Year><Month>05</Month><Day>12</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-294X</ISSN><JournalIssue CitedMedium="Internet"><Volume>26</Volume><Issue>7</Issue><PubDate><Year>2017</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Molecular ecology</Title><ISOAbbreviation>Mol Ecol</ISOAbbreviation></Journal><ArticleTitle>Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes.</ArticleTitle><Pagination><MedlinePgn>2063-2076</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/mec.13892</ELocationID><Abstract><AbstractText>Recent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with the roots of pine trees. We used genomic data from 55 individuals in seven locations across North America to perform genome scans to detect signatures of positive selection and assess whether temperature and precipitation were associated with genetic differentiation. We found that S. brevipes exhibited overall strong population differentiation, with potential admixture in Canadian populations. This species also displayed genomic signatures of positive selection as well as genomic sites significantly associated with distinct climatic regimes and abiotic environmental parameters. These genomic regions included genes involved in transmembrane transport of substances and helicase activity potentially involved in cold stress response. Our study sheds light on large-scale environmental adaptation in fungi by identifying putative adaptive genes and providing a framework to further investigate the genetic basis of fungal adaptation.</AbstractText><CopyrightInformation>© 2016 John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Branco</LastName><ForeName>Sara</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bi</LastName><ForeName>Ke</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, 94720, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liao</LastName><ForeName>Hui-Ling</ForeName><Initials>HL</Initials><AffiliationInfo><Affiliation>North Florida Research and Education Center, University of Florida, Quincy, FL, 32351, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gladieux</LastName><ForeName>Pierre</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>INRA, UMR BGPI, Montpellier, 34398, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Badouin</LastName><ForeName>Hélène</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ellison</LastName><ForeName>Christopher E</ForeName><Initials>CE</Initials><AffiliationInfo><Affiliation>Department of Genetics, Rutgers University, Piscataway, NJ, 08901, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nguyen</LastName><ForeName>Nhu H</ForeName><Initials>NH</Initials><AffiliationInfo><Affiliation>Department of Tropical Plant and Soil Sciences, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vilgalys</LastName><ForeName>Rytas</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Biology, Duke University, Durham, NC, 27708, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Peay</LastName><ForeName>Kabir G</ForeName><Initials>KG</Initials><AffiliationInfo><Affiliation>Department of Biology, Stanford University, Stanford, CA, 94305, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Taylor</LastName><ForeName>John W</ForeName><Initials>JW</Initials><AffiliationInfo><Affiliation>Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bruns</LastName><ForeName>Thomas D</ForeName><Initials>TD</Initials><AffiliationInfo><Affiliation>Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>S10 RR027303</GrantID><Acronym>RR</Acronym><Agency>NCRR NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>S10 RR029668</GrantID><Acronym>RR</Acronym><Agency>NCRR NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>11</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Ecol</MedlineTA><NlmUniqueID>9214478</NlmUniqueID><ISSNLinking>0962-1083</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004271">DNA, Fungal</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000222" MajorTopicYN="N">Adaptation, Physiological</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000363" MajorTopicYN="N">Agaricales</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001487" MajorTopicYN="N">Basidiomycota</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002170" MajorTopicYN="N">Canada</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002980" MajorTopicYN="N">Climate</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058639" MajorTopicYN="N">Cold-Shock Response</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004271" MajorTopicYN="N">DNA, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005828" MajorTopicYN="Y">Genetics, Population</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016681" MajorTopicYN="N">Genome, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015810" MajorTopicYN="N">Linkage Disequilibrium</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009656" MajorTopicYN="N">North America</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D028223" MajorTopicYN="N">Pinus</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011891" MajorTopicYN="N">Rain</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012641" MajorTopicYN="Y">Selection, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012914" MajorTopicYN="N">Snow</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013696" MajorTopicYN="N">Temperature</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Suillus brevipes
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