Genetic variation and phylogenetic relationships of the ectomycorrhizal Floccularia luteovirens on the Qinghai-Tibet Plateau.
Identifieur interne : 000C16 ( Main/Corpus ); précédent : 000C15; suivant : 000C17Genetic variation and phylogenetic relationships of the ectomycorrhizal Floccularia luteovirens on the Qinghai-Tibet Plateau.
Auteurs : Rui Xing ; Qing-Bo Gao ; Fa-Qi Zhang ; Peng-Cheng Fu ; Jiu-Li Wang ; Hui-Ying Yan ; Shi-Long ChenSource :
- Journal of microbiology (Seoul, Korea) [ 1976-3794 ] ; 2017.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Peptide Elongation Factor 1, RNA Polymerase I.
- classification : Armillaria, Mycorrhizae.
- genetics : Armillaria, Mycorrhizae.
- Cluster Analysis, Genetic Variation, Phylogeny, Sequence Analysis, DNA, Tibet.
Abstract
Floccularia luteovirens, as an ectomycorrhizal fungus, is widely distributed in the Qinghai-Tibet Plateau. As an edible fungus, it is famous for its unique flavor. Former studies mainly focus on the chemical composition and genetic structure of this species. However, the phylogenetic relationship between genotypes remains unknown. In this study, the genetic variation and phylogenetic relationship between the genotypes of F. luteovirens in Qinghai-Tibet Plateau was estimated through the analysis on two protein-coding genes (rpb1 and ef-1α) from 398 individuals collected from 24 wild populations. The sample covered the entire range of this species during all the growth seasons from 2011 to 2015. 13 genotypes were detected and moderate genetic diversity was revealed. Based on the results of network analysis, the maximum likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) analyses, the genotypes H-1, H-4, H-6, H-8, H-10, and H-11 were grouped into one clade. Additionally, a relatively higher genotype diversity (average h value is 0.722) and unique genotypes in the northeast edge of Qinghai- Tibet plateau have been found, combined with the results of mismatch analysis and neutrality tests indicated that Southeast Qinghai-Tibet plateau was a refuge for F. luteovirens during the historical geological or climatic events (uplifting of the Qinghai-Tibet Plateau or Last Glacial Maximum). Furthermore, the present distribution of the species on the Qinghai-Tibet plateau has resulted from the recent population expansion. Our findings provide a foundation for the future study of the evolutionary history and the speciation of this species.
DOI: 10.1007/s12275-017-7101-4
PubMed: 28674972
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China.</nlm:affiliation></affiliation></author><author><name sortKey="Yan, Hui Ying" sort="Yan, Hui Ying" uniqKey="Yan H" first="Hui-Ying" last="Yan">Hui-Ying Yan</name><affiliation><nlm:affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Shi Long" sort="Chen, Shi Long" uniqKey="Chen S" first="Shi-Long" last="Chen">Shi-Long Chen</name><affiliation><nlm:affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China. slchen@nwipb.cas.cn.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:28674972</idno><idno type="pmid">28674972</idno><idno type="doi">10.1007/s12275-017-7101-4</idno><idno type="wicri:Area/Main/Corpus">000C16</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000C16</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Genetic variation and phylogenetic relationships of the ectomycorrhizal Floccularia luteovirens on the Qinghai-Tibet Plateau.</title><author><name sortKey="Xing, Rui" sort="Xing, Rui" uniqKey="Xing R" first="Rui" last="Xing">Rui Xing</name><affiliation><nlm:affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Key Laboratory of Crop Molecular Breeding of Qinghai Provice, Qinghai, P. R. China.</nlm:affiliation></affiliation></author><author><name sortKey="Gao, Qing Bo" sort="Gao, Qing Bo" uniqKey="Gao Q" first="Qing-Bo" last="Gao">Qing-Bo Gao</name><affiliation><nlm:affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Fa Qi" sort="Zhang, Fa Qi" uniqKey="Zhang F" first="Fa-Qi" last="Zhang">Fa-Qi Zhang</name><affiliation><nlm:affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Key Laboratory of Eco-Environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, P. R. China.</nlm:affiliation></affiliation></author><author><name sortKey="Fu, Peng Cheng" sort="Fu, Peng Cheng" uniqKey="Fu P" first="Peng-Cheng" last="Fu">Peng-Cheng Fu</name><affiliation><nlm:affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Jiu Li" sort="Wang, Jiu Li" uniqKey="Wang J" first="Jiu-Li" last="Wang">Jiu-Li Wang</name><affiliation><nlm:affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.</nlm:affiliation></affiliation></author><author><name sortKey="Yan, Hui Ying" sort="Yan, Hui Ying" uniqKey="Yan H" first="Hui-Ying" last="Yan">Hui-Ying Yan</name><affiliation><nlm:affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Shi Long" sort="Chen, Shi Long" uniqKey="Chen S" first="Shi-Long" last="Chen">Shi-Long Chen</name><affiliation><nlm:affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China. slchen@nwipb.cas.cn.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Journal of microbiology (Seoul, Korea)</title><idno type="eISSN">1976-3794</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Armillaria (classification)</term><term>Armillaria (genetics)</term><term>Cluster Analysis (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Mycorrhizae (classification)</term><term>Mycorrhizae (genetics)</term><term>Peptide Elongation Factor 1 (genetics)</term><term>Phylogeny (MeSH)</term><term>RNA Polymerase I (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Tibet (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Peptide Elongation Factor 1</term><term>RNA Polymerase I</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Armillaria</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Armillaria</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cluster Analysis</term><term>Genetic Variation</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term><term>Tibet</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Floccularia luteovirens, as an ectomycorrhizal fungus, is widely distributed in the Qinghai-Tibet Plateau. As an edible fungus, it is famous for its unique flavor. Former studies mainly focus on the chemical composition and genetic structure of this species. However, the phylogenetic relationship between genotypes remains unknown. In this study, the genetic variation and phylogenetic relationship between the genotypes of F. luteovirens in Qinghai-Tibet Plateau was estimated through the analysis on two protein-coding genes (rpb1 and ef-1α) from 398 individuals collected from 24 wild populations. The sample covered the entire range of this species during all the growth seasons from 2011 to 2015. 13 genotypes were detected and moderate genetic diversity was revealed. Based on the results of network analysis, the maximum likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) analyses, the genotypes H-1, H-4, H-6, H-8, H-10, and H-11 were grouped into one clade. Additionally, a relatively higher genotype diversity (average h value is 0.722) and unique genotypes in the northeast edge of Qinghai- Tibet plateau have been found, combined with the results of mismatch analysis and neutrality tests indicated that Southeast Qinghai-Tibet plateau was a refuge for F. luteovirens during the historical geological or climatic events (uplifting of the Qinghai-Tibet Plateau or Last Glacial Maximum). Furthermore, the present distribution of the species on the Qinghai-Tibet plateau has resulted from the recent population expansion. Our findings provide a foundation for the future study of the evolutionary history and the speciation of this species.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28674972</PMID><DateCompleted><Year>2018</Year><Month>02</Month><Day>01</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1976-3794</ISSN><JournalIssue CitedMedium="Internet"><Volume>55</Volume><Issue>8</Issue><PubDate><Year>2017</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Journal of microbiology (Seoul, Korea)</Title><ISOAbbreviation>J Microbiol</ISOAbbreviation></Journal><ArticleTitle>Genetic variation and phylogenetic relationships of the ectomycorrhizal Floccularia luteovirens on the Qinghai-Tibet Plateau.</ArticleTitle><Pagination><MedlinePgn>600-606</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s12275-017-7101-4</ELocationID><Abstract><AbstractText>Floccularia luteovirens, as an ectomycorrhizal fungus, is widely distributed in the Qinghai-Tibet Plateau. As an edible fungus, it is famous for its unique flavor. Former studies mainly focus on the chemical composition and genetic structure of this species. However, the phylogenetic relationship between genotypes remains unknown. In this study, the genetic variation and phylogenetic relationship between the genotypes of F. luteovirens in Qinghai-Tibet Plateau was estimated through the analysis on two protein-coding genes (rpb1 and ef-1α) from 398 individuals collected from 24 wild populations. The sample covered the entire range of this species during all the growth seasons from 2011 to 2015. 13 genotypes were detected and moderate genetic diversity was revealed. Based on the results of network analysis, the maximum likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) analyses, the genotypes H-1, H-4, H-6, H-8, H-10, and H-11 were grouped into one clade. Additionally, a relatively higher genotype diversity (average h value is 0.722) and unique genotypes in the northeast edge of Qinghai- Tibet plateau have been found, combined with the results of mismatch analysis and neutrality tests indicated that Southeast Qinghai-Tibet plateau was a refuge for F. luteovirens during the historical geological or climatic events (uplifting of the Qinghai-Tibet Plateau or Last Glacial Maximum). Furthermore, the present distribution of the species on the Qinghai-Tibet plateau has resulted from the recent population expansion. Our findings provide a foundation for the future study of the evolutionary history and the speciation of this species.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xing</LastName><ForeName>Rui</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Crop Molecular Breeding of Qinghai Provice, Qinghai, P. R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>Qing-Bo</ForeName><Initials>QB</Initials><AffiliationInfo><Affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Fa-Qi</ForeName><Initials>FQ</Initials><AffiliationInfo><Affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Eco-Environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, P. R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fu</LastName><ForeName>Peng-Cheng</ForeName><Initials>PC</Initials><AffiliationInfo><Affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Jiu-Li</ForeName><Initials>JL</Initials><AffiliationInfo><Affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yan</LastName><ForeName>Hui-Ying</ForeName><Initials>HY</Initials><AffiliationInfo><Affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Shi-Long</ForeName><Initials>SL</Initials><AffiliationInfo><Affiliation>Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai, 810001, P. R. China. slchen@nwipb.cas.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>07</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>Korea (South)</Country><MedlineTA>J Microbiol</MedlineTA><NlmUniqueID>9703165</NlmUniqueID><ISSNLinking>1225-8873</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020648">Peptide Elongation Factor 1</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.7.7.6</RegistryNumber><NameOfSubstance UI="D012318">RNA Polymerase I</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D055392" MajorTopicYN="N">Armillaria</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020648" MajorTopicYN="N">Peptide Elongation Factor 1</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="Y">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012318" MajorTopicYN="N">RNA Polymerase I</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018609" MajorTopicYN="N">Tibet</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Floccularia luteovirens</Keyword><Keyword MajorTopicYN="N">Qinghai-Tibet Plateau</Keyword><Keyword MajorTopicYN="N">phylogenetics</Keyword><Keyword MajorTopicYN="N">phylogeography</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>03</Month><Day>08</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>06</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2017</Year><Month>06</Month><Day>01</Day></PubMedPubDate><PubMedPubDate 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