Increased phylogenetic resolution within the ecologically important Rhizopogon subgenus Amylopogon using 10 anonymous nuclear loci.
Identifieur interne : 000D15 ( Main/Exploration ); précédent : 000D14; suivant : 000D16Increased phylogenetic resolution within the ecologically important Rhizopogon subgenus Amylopogon using 10 anonymous nuclear loci.
Auteurs : Nicholas J. Dowie [États-Unis] ; Lisa C. Grubisha [États-Unis] ; Brent A. Burton [États-Unis] ; Matthew R. Klooster [États-Unis] ; Steven L. Miller [États-Unis]Source :
- Mycologia [ 0027-5514 ] ; 2017.
Descripteurs français
- KwdFr :
- ADN fongique (composition chimique), ADN fongique (génétique), Analyse de regroupements (MeSH), Analyse de séquence d'ADN (MeSH), Basidiomycota (classification), Basidiomycota (génétique), Ericaceae (microbiologie), Espaceur de l'ADN ribosomique (composition chimique), Espaceur de l'ADN ribosomique (génétique), Mycorhizes (classification), Mycorhizes (génétique), Phylogenèse (MeSH), États-Unis (MeSH).
- MESH :
- composition chimique : ADN fongique, Basidiomycota, Espaceur de l'ADN ribosomique, Mycorhizes.
- génétique : ADN fongique, Basidiomycota, Espaceur de l'ADN ribosomique, Mycorhizes.
- microbiologie : Ericaceae.
- Analyse de regroupements, Analyse de séquence d'ADN, Phylogenèse, États-Unis.
English descriptors
- KwdEn :
- Basidiomycota (classification), Basidiomycota (genetics), Cluster Analysis (MeSH), DNA, Fungal (chemistry), DNA, Fungal (genetics), DNA, Ribosomal Spacer (chemistry), DNA, Ribosomal Spacer (genetics), Ericaceae (microbiology), Mycorrhizae (classification), Mycorrhizae (genetics), Phylogeny (MeSH), Sequence Analysis, DNA (MeSH), United States (MeSH).
- MESH :
- chemical , chemistry : DNA, Fungal, DNA, Ribosomal Spacer.
- classification : Basidiomycota, Mycorrhizae.
- genetics : Basidiomycota, DNA, Fungal, DNA, Ribosomal Spacer, Mycorrhizae.
- microbiology : Ericaceae.
- Cluster Analysis, Phylogeny, Sequence Analysis, DNA, United States.
Abstract
Rhizopogon species are ecologically significant ectomycorrhizal fungi in conifer ecosystems. The importance of this system merits the development and utilization of a more robust set of molecular markers specifically designed to evaluate their evolutionary ecology. Anonymous nuclear loci (ANL) were developed for R. subgenus Amylopogon. Members of this subgenus occur throughout the United States and are exclusive fungal symbionts associated with Pterospora andromedea, a threatened mycoheterotrophic plant endemic to disjunct eastern and western regions of North America. Candidate ANL were developed from 454 shotgun pyrosequencing and assessed for positive amplification across targeted species, sequencing success, and recovery of phylogenetically informative sites. Ten ANL were successfully developed and were subsequently used to sequence representative taxa, herbaria holotype and paratype specimens in R. subgenus Amylopogon. Phylogenetic reconstructions were performed on individual and concatenated data sets by Bayesian inference and maximum likelihood methods. Phylogenetic analyses of these 10 ANL were compared with a phylogeny traditionally constructed using the universal fungal barcode nuc rDNA ITS1-5.8S-ITS2 region (ITS). The resulting ANL phylogeny was consistent with most of the species designations delineated by ITS. However, the ANL phylogeny provided much greater phylogenetic resolution, yielding new evidence for cryptic species within previously defined species of R. subgenus Amylopogon. Additionally, the rooted ANL phylogeny provided an alternate topology to the ITS phylogeny, which inferred a novel set of evolutionary relationships not identified in prior phylogenetic studies.
DOI: 10.1080/00275514.2017.1285165
PubMed: 28402794
Affiliations:
Links toward previous steps (curation, corpus...)
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Miller</name><affiliation wicri:level="2"><nlm:affiliation>a Department of Botany , University of Wyoming , 1000 University Avenue, Laramie , Wyoming 82071.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Wyoming</region></placeName><wicri:cityArea>a Department of Botany , University of Wyoming , 1000 University Avenue, Laramie </wicri:cityArea></affiliation></author></analytic><series><title level="j">Mycologia</title><idno type="ISSN">0027-5514</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Basidiomycota (classification)</term><term>Basidiomycota (genetics)</term><term>Cluster Analysis (MeSH)</term><term>DNA, Fungal (chemistry)</term><term>DNA, Fungal (genetics)</term><term>DNA, Ribosomal Spacer (chemistry)</term><term>DNA, Ribosomal Spacer (genetics)</term><term>Ericaceae (microbiology)</term><term>Mycorrhizae (classification)</term><term>Mycorrhizae (genetics)</term><term>Phylogeny (MeSH)</term><term>Sequence Analysis, DNA (MeSH)</term><term>United States (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN fongique (composition chimique)</term><term>ADN fongique (génétique)</term><term>Analyse de regroupements (MeSH)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Basidiomycota (classification)</term><term>Basidiomycota (génétique)</term><term>Ericaceae (microbiologie)</term><term>Espaceur de l'ADN ribosomique (composition chimique)</term><term>Espaceur de l'ADN ribosomique (génétique)</term><term>Mycorhizes (classification)</term><term>Mycorhizes (génétique)</term><term>Phylogenèse (MeSH)</term><term>États-Unis (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA, Fungal</term><term>DNA, Ribosomal Spacer</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Basidiomycota</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>ADN fongique</term><term>Basidiomycota</term><term>Espaceur de l'ADN ribosomique</term><term>Mycorhizes</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Basidiomycota</term><term>DNA, Fungal</term><term>DNA, Ribosomal Spacer</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN fongique</term><term>Basidiomycota</term><term>Espaceur de l'ADN ribosomique</term><term>Mycorhizes</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Ericaceae</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Ericaceae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cluster Analysis</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term><term>United States</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de regroupements</term><term>Analyse de séquence d'ADN</term><term>Phylogenèse</term><term>États-Unis</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Rhizopogon species are ecologically significant ectomycorrhizal fungi in conifer ecosystems. The importance of this system merits the development and utilization of a more robust set of molecular markers specifically designed to evaluate their evolutionary ecology. Anonymous nuclear loci (ANL) were developed for R. subgenus Amylopogon. Members of this subgenus occur throughout the United States and are exclusive fungal symbionts associated with Pterospora andromedea, a threatened mycoheterotrophic plant endemic to disjunct eastern and western regions of North America. Candidate ANL were developed from 454 shotgun pyrosequencing and assessed for positive amplification across targeted species, sequencing success, and recovery of phylogenetically informative sites. Ten ANL were successfully developed and were subsequently used to sequence representative taxa, herbaria holotype and paratype specimens in R. subgenus Amylopogon. Phylogenetic reconstructions were performed on individual and concatenated data sets by Bayesian inference and maximum likelihood methods. Phylogenetic analyses of these 10 ANL were compared with a phylogeny traditionally constructed using the universal fungal barcode nuc rDNA ITS1-5.8S-ITS2 region (ITS). The resulting ANL phylogeny was consistent with most of the species designations delineated by ITS. However, the ANL phylogeny provided much greater phylogenetic resolution, yielding new evidence for cryptic species within previously defined species of R. subgenus Amylopogon. Additionally, the rooted ANL phylogeny provided an alternate topology to the ITS phylogeny, which inferred a novel set of evolutionary relationships not identified in prior phylogenetic studies.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28402794</PMID><DateCompleted><Year>2018</Year><Month>05</Month><Day>29</Day></DateCompleted><DateRevised><Year>2018</Year><Month>06</Month><Day>18</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0027-5514</ISSN><JournalIssue CitedMedium="Print"><Volume>109</Volume><Issue>1</Issue><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>Mycologia</Title><ISOAbbreviation>Mycologia</ISOAbbreviation></Journal><ArticleTitle>Increased phylogenetic resolution within the ecologically important Rhizopogon subgenus Amylopogon using 10 anonymous nuclear loci.</ArticleTitle><Pagination><MedlinePgn>35-45</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/00275514.2017.1285165</ELocationID><Abstract><AbstractText>Rhizopogon species are ecologically significant ectomycorrhizal fungi in conifer ecosystems. The importance of this system merits the development and utilization of a more robust set of molecular markers specifically designed to evaluate their evolutionary ecology. Anonymous nuclear loci (ANL) were developed for R. subgenus Amylopogon. Members of this subgenus occur throughout the United States and are exclusive fungal symbionts associated with Pterospora andromedea, a threatened mycoheterotrophic plant endemic to disjunct eastern and western regions of North America. Candidate ANL were developed from 454 shotgun pyrosequencing and assessed for positive amplification across targeted species, sequencing success, and recovery of phylogenetically informative sites. Ten ANL were successfully developed and were subsequently used to sequence representative taxa, herbaria holotype and paratype specimens in R. subgenus Amylopogon. Phylogenetic reconstructions were performed on individual and concatenated data sets by Bayesian inference and maximum likelihood methods. Phylogenetic analyses of these 10 ANL were compared with a phylogeny traditionally constructed using the universal fungal barcode nuc rDNA ITS1-5.8S-ITS2 region (ITS). The resulting ANL phylogeny was consistent with most of the species designations delineated by ITS. However, the ANL phylogeny provided much greater phylogenetic resolution, yielding new evidence for cryptic species within previously defined species of R. subgenus Amylopogon. Additionally, the rooted ANL phylogeny provided an alternate topology to the ITS phylogeny, which inferred a novel set of evolutionary relationships not identified in prior phylogenetic studies.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Dowie</LastName><ForeName>Nicholas J</ForeName><Initials>NJ</Initials><AffiliationInfo><Affiliation>a Department of Botany , University of Wyoming , 1000 University Avenue, Laramie , Wyoming 82071.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grubisha</LastName><ForeName>Lisa C</ForeName><Initials>LC</Initials><AffiliationInfo><Affiliation>b Department of Natural and Applied Sciences , University of Wisconsin-Green Bay , 2420 Nicolet Drive, Green Bay, Wisconsin 54311.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Burton</LastName><ForeName>Brent A</ForeName><Initials>BA</Initials><AffiliationInfo><Affiliation>a Department of Botany , University of Wyoming , 1000 University Avenue, Laramie , Wyoming 82071.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Klooster</LastName><ForeName>Matthew R</ForeName><Initials>MR</Initials><AffiliationInfo><Affiliation>c Centre College , 600 West Walnut Street, Young Hall 243, Danville , Kentucky 40422.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Miller</LastName><ForeName>Steven L</ForeName><Initials>SL</Initials><AffiliationInfo><Affiliation>a Department of Botany , University of Wyoming , 1000 University Avenue, Laramie , Wyoming 82071.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>01</Month><Day>31</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mycologia</MedlineTA><NlmUniqueID>0400764</NlmUniqueID><ISSNLinking>0027-5514</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004271">DNA, Fungal</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D021903">DNA, Ribosomal Spacer</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001487" MajorTopicYN="N">Basidiomycota</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="D004271" MajorTopicYN="N">DNA, Fungal</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D021903" MajorTopicYN="N">DNA, Ribosomal Spacer</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D029791" MajorTopicYN="N">Ericaceae</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></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="D010802" MajorTopicYN="Y">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014481" MajorTopicYN="N">United States</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">ANL</Keyword><Keyword MajorTopicYN="Y">Amylopogon</Keyword><Keyword MajorTopicYN="Y">ITS</Keyword><Keyword MajorTopicYN="Y">Pterospora andromedea</Keyword><Keyword MajorTopicYN="Y">Rhizopogon</Keyword><Keyword MajorTopicYN="Y">anonymous nuclear loci</Keyword><Keyword MajorTopicYN="Y">phylogenetics</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>4</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>4</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>5</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28402794</ArticleId><ArticleId IdType="doi">10.1080/00275514.2017.1285165</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Kentucky</li><li>Wisconsin</li><li>Wyoming</li></region></list><tree><country name="États-Unis"><region name="Wyoming"><name sortKey="Dowie, Nicholas J" sort="Dowie, Nicholas J" uniqKey="Dowie N" first="Nicholas J" last="Dowie">Nicholas J. Dowie</name></region><name sortKey="Burton, Brent A" sort="Burton, Brent A" uniqKey="Burton B" first="Brent A" last="Burton">Brent A. Burton</name><name sortKey="Grubisha, Lisa C" sort="Grubisha, Lisa C" uniqKey="Grubisha L" first="Lisa C" last="Grubisha">Lisa C. Grubisha</name><name sortKey="Klooster, Matthew R" sort="Klooster, Matthew R" uniqKey="Klooster M" first="Matthew R" last="Klooster">Matthew R. Klooster</name><name sortKey="Miller, Steven L" sort="Miller, Steven L" uniqKey="Miller S" first="Steven L" last="Miller">Steven L. Miller</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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