Fungal heavy metal adaptation through single nucleotide polymorphisms and copy-number variation.
Identifieur interne : 000189 ( Main/Exploration ); précédent : 000188; suivant : 000190Fungal heavy metal adaptation through single nucleotide polymorphisms and copy-number variation.
Auteurs : Anna L. Bazzicalupo [États-Unis] ; Joske Ruytinx [Belgique] ; Yi-Hong Ke [États-Unis] ; Laura Coninx [Belgique] ; Jan V. Colpaert [Belgique] ; Nhu H. Nguyen [États-Unis] ; Rytas Vilgalys [États-Unis] ; Sara Branco [États-Unis]Source :
- Molecular ecology [ 1365-294X ] ; 2020.
Abstract
Human-altered environments can shape the evolution of organisms. Fungi are no exception, although little is known about how they withstand anthropogenic pollution. Here, we document adaptation in the mycorrhizal fungus Suillus luteus driven by soil heavy metal contamination. Genome scans across individuals from recently polluted and nearby unpolluted soils in Belgium revealed low divergence across isolates and no evidence of population structure based on soil type. However, we detected single nucleotide polymorphism divergence and gene copy-number variation, with different genetic combinations potentially conferring the ability to persist in contaminated soils. Variants were shared across the population but found to be under selection in isolates exposed to pollution and located across the genome, including in genes involved in metal exclusion, storage, immobilization and reactive oxygen species detoxification. Together, our results point to S. luteus undergoing the initial steps of adaptive divergence and contribute to understanding the processes underlying local adaptation under strong environmental selection.
DOI: 10.1111/mec.15618
PubMed: 32866320
Affiliations:
- Belgique, États-Unis
- Caroline du Nord, Colorado, Hawaï, Montana, Région de Bruxelles-Capitale
- Bruxelles
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Bazzicalupo</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology and Immunology, Montana State University, Bozeman, MT</wicri:regionArea><placeName><region type="state">Montana</region></placeName></affiliation></author><author><name sortKey="Ruytinx, Joske" sort="Ruytinx, Joske" uniqKey="Ruytinx J" first="Joske" last="Ruytinx">Joske Ruytinx</name><affiliation wicri:level="3"><nlm:affiliation>Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels</wicri:regionArea><placeName><settlement type="city">Bruxelles</settlement><region nuts="2">Région de Bruxelles-Capitale</region></placeName></affiliation></author><author><name sortKey="Ke, Yi Hong" sort="Ke, Yi Hong" uniqKey="Ke Y" first="Yi-Hong" last="Ke">Yi-Hong Ke</name><affiliation wicri:level="2"><nlm:affiliation>Biology Department, Duke University, Durham, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biology Department, Duke University, Durham, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation></author><author><name sortKey="Coninx, Laura" sort="Coninx, Laura" uniqKey="Coninx L" first="Laura" last="Coninx">Laura Coninx</name><affiliation wicri:level="1"><nlm:affiliation>Biology Department, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Biology Department, Centre for Environmental Sciences, Hasselt University, Diepenbeek</wicri:regionArea><wicri:noRegion>Diepenbeek</wicri:noRegion></affiliation></author><author><name sortKey="Colpaert, Jan V" sort="Colpaert, Jan V" uniqKey="Colpaert J" first="Jan V" last="Colpaert">Jan V. Colpaert</name><affiliation wicri:level="1"><nlm:affiliation>Biology Department, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Biology Department, Centre for Environmental Sciences, Hasselt University, Diepenbeek</wicri:regionArea><wicri:noRegion>Diepenbeek</wicri:noRegion></affiliation></author><author><name sortKey="Nguyen, Nhu H" sort="Nguyen, Nhu H" uniqKey="Nguyen N" first="Nhu H" last="Nguyen">Nhu H. Nguyen</name><affiliation wicri:level="2"><nlm:affiliation>Department of Tropical Plant and Soil Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Tropical Plant and Soil Sciences, University of Hawai'i at Mānoa, Honolulu, HI</wicri:regionArea><placeName><region type="state">Hawaï</region></placeName></affiliation></author><author><name sortKey="Vilgalys, Rytas" sort="Vilgalys, Rytas" uniqKey="Vilgalys R" first="Rytas" last="Vilgalys">Rytas Vilgalys</name><affiliation wicri:level="2"><nlm:affiliation>Biology Department, Duke University, Durham, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biology Department, Duke University, Durham, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation></author><author><name sortKey="Branco, Sara" sort="Branco, Sara" uniqKey="Branco S" first="Sara" last="Branco">Sara Branco</name><affiliation wicri:level="2"><nlm:affiliation>Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Integrative Biology, University of Colorado Denver, Denver, CO</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation></author></analytic><series><title level="j">Molecular ecology</title><idno type="eISSN">1365-294X</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">Human-altered environments can shape the evolution of organisms. Fungi are no exception, although little is known about how they withstand anthropogenic pollution. Here, we document adaptation in the mycorrhizal fungus Suillus luteus driven by soil heavy metal contamination. Genome scans across individuals from recently polluted and nearby unpolluted soils in Belgium revealed low divergence across isolates and no evidence of population structure based on soil type. However, we detected single nucleotide polymorphism divergence and gene copy-number variation, with different genetic combinations potentially conferring the ability to persist in contaminated soils. Variants were shared across the population but found to be under selection in isolates exposed to pollution and located across the genome, including in genes involved in metal exclusion, storage, immobilization and reactive oxygen species detoxification. Together, our results point to S. luteus undergoing the initial steps of adaptive divergence and contribute to understanding the processes underlying local adaptation under strong environmental selection.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32866320</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>15</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-294X</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Aug</Month><Day>31</Day></PubDate></JournalIssue><Title>Molecular ecology</Title><ISOAbbreviation>Mol Ecol</ISOAbbreviation></Journal><ArticleTitle>Fungal heavy metal adaptation through single nucleotide polymorphisms and copy-number variation.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1111/mec.15618</ELocationID><Abstract><AbstractText>Human-altered environments can shape the evolution of organisms. Fungi are no exception, although little is known about how they withstand anthropogenic pollution. Here, we document adaptation in the mycorrhizal fungus Suillus luteus driven by soil heavy metal contamination. Genome scans across individuals from recently polluted and nearby unpolluted soils in Belgium revealed low divergence across isolates and no evidence of population structure based on soil type. However, we detected single nucleotide polymorphism divergence and gene copy-number variation, with different genetic combinations potentially conferring the ability to persist in contaminated soils. Variants were shared across the population but found to be under selection in isolates exposed to pollution and located across the genome, including in genes involved in metal exclusion, storage, immobilization and reactive oxygen species detoxification. Together, our results point to S. luteus undergoing the initial steps of adaptive divergence and contribute to understanding the processes underlying local adaptation under strong environmental selection.</AbstractText><CopyrightInformation>© 2020 John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bazzicalupo</LastName><ForeName>Anna L</ForeName><Initials>AL</Initials><Identifier Source="ORCID">https://orcid.org/0000-0001-5845-9517</Identifier><AffiliationInfo><Affiliation>Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ruytinx</LastName><ForeName>Joske</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ke</LastName><ForeName>Yi-Hong</ForeName><Initials>YH</Initials><AffiliationInfo><Affiliation>Biology Department, Duke University, Durham, NC, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Coninx</LastName><ForeName>Laura</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Biology Department, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Colpaert</LastName><ForeName>Jan V</ForeName><Initials>JV</Initials><AffiliationInfo><Affiliation>Biology Department, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.</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, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vilgalys</LastName><ForeName>Rytas</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Biology Department, Duke University, Durham, NC, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Branco</LastName><ForeName>Sara</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>502931</GrantID><Agency>Joint Genome Institute Community Science Program</Agency><Country></Country></Grant><Grant><GrantID>DEB-1554181</GrantID><Agency>NSF</Agency><Country></Country></Grant><Grant><GrantID>141461</GrantID><Agency>Flanders Innovation & Entrepreneurships PhD fellowship</Agency><Country></Country></Grant><Grant><Agency>Hawaii's Agricultural Experiment Station</Agency><Country></Country></Grant><Grant><Agency>Montana's Agricultural Experiment Station</Agency><Country></Country></Grant><Grant><GrantID>G079213N</GrantID><Agency>Fonds Wetenschappelijk Onderzoek</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>08</Month><Day>31</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Ecol</MedlineTA><NlmUniqueID>9214478</NlmUniqueID><ISSNLinking>0962-1083</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Suillus luteus
</Keyword><Keyword MajorTopicYN="N">fungi</Keyword><Keyword MajorTopicYN="N">gene flow</Keyword><Keyword MajorTopicYN="N">heavy metal soil</Keyword><Keyword MajorTopicYN="N">mycorrhizal</Keyword><Keyword MajorTopicYN="N">pollution</Keyword><Keyword MajorTopicYN="N">polygenic adaptation</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>12</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>08</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>9</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>9</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>9</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32866320</ArticleId><ArticleId IdType="doi">10.1111/mec.15618</ArticleId></ArticleIdList><ReferenceList><Title>REFERENCES</Title><Reference><Citation>Adriaensen, K., Vangronsveld, J., & Colpaert, J. 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