Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples - an example of saddle fungi.
Identifieur interne : 001437 ( Main/Corpus ); précédent : 001436; suivant : 001438Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples - an example of saddle fungi.
Auteurs : Jonathan Hwang ; Qi Zhao ; Zhu L. Yang ; Zheng Wang ; Jeffrey P. TownsendSource :
- Environmental microbiology reports [ 1758-2229 ] ; 2015.
English descriptors
- KwdEn :
- Ascomycota (classification), Ascomycota (genetics), Ascomycota (isolation & purification), Biodiversity (MeSH), Biological Evolution (MeSH), Cluster Analysis (MeSH), DNA, Fungal (chemistry), DNA, Fungal (genetics), DNA, Ribosomal Spacer (chemistry), DNA, Ribosomal Spacer (genetics), Ecosystem (MeSH), Mycorrhizae (classification), Mycorrhizae (genetics), Mycorrhizae (isolation & purification), Phylogeny (MeSH), Plants (microbiology), Sequence Analysis, DNA (MeSH), Soil Microbiology (MeSH).
- MESH :
- chemical , chemistry : DNA, Fungal, DNA, Ribosomal Spacer.
- classification : Ascomycota, Mycorrhizae.
- genetics : Ascomycota, DNA, Fungal, DNA, Ribosomal Spacer, Mycorrhizae.
- isolation & purification : Ascomycota, Mycorrhizae.
- microbiology : Plants.
- Biodiversity, Biological Evolution, Cluster Analysis, Ecosystem, Phylogeny, Sequence Analysis, DNA, Soil Microbiology.
Abstract
The relation between ecological and genetic divergence of Helvella species (saddle fungi) has been perplexing. While a few species have been clearly demonstrated to be ectomycorrhizal fungi, ecological roles of many other species have been controversial, alternately considered as either saprotrophic or mycorrhizal. We applied SATé to build an inclusive deoxyribonucleic acid sequence alignment for the internal transcribed spacers (ITS) of annotated Helvella species and related environmental sequences. Phylogenetic informativeness of ITS and its regions were assessed using PhyDesign. Mycorrhizal lineages present a diversity of ecology, host type and geographic distribution. In two Helvella clades, no Helvella ITS sequences were recovered from root tips. Inclusion of environmental sequences in the ITS phylogeny from these sequences has the potential to link these data and reveal Helvella ecology. This study can serve as a model for revealing the diversity of relationships between unculturable fungi and their potential plant hosts. How non-mycorrhizal life styles within Helvella evolved will require expanded metagenomic investigation of soil and other environmental samples along with study of Helvella genomes.
DOI: 10.1111/1758-2229.12303
PubMed: 26033481
Links to Exploration step
pubmed:26033481Le document en format XML
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Yang</name><affiliation><nlm:affiliation>Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Zheng" sort="Wang, Zheng" uniqKey="Wang Z" first="Zheng" last="Wang">Zheng Wang</name><affiliation><nlm:affiliation>Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Townsend, Jeffrey P" sort="Townsend, Jeffrey P" uniqKey="Townsend J" first="Jeffrey P" last="Townsend">Jeffrey P. Townsend</name><affiliation><nlm:affiliation>Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Program in Microbiology, Yale University, New Haven, CT 06520, USA.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26033481</idno><idno type="pmid">26033481</idno><idno type="doi">10.1111/1758-2229.12303</idno><idno type="wicri:Area/Main/Corpus">001437</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001437</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples - an example of saddle fungi.</title><author><name sortKey="Hwang, Jonathan" sort="Hwang, Jonathan" uniqKey="Hwang J" first="Jonathan" last="Hwang">Jonathan Hwang</name><affiliation><nlm:affiliation>Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zhao, Qi" sort="Zhao, Qi" uniqKey="Zhao Q" first="Qi" last="Zhao">Qi Zhao</name><affiliation><nlm:affiliation>Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.</nlm:affiliation></affiliation></author><author><name sortKey="Yang, Zhu L" sort="Yang, Zhu L" uniqKey="Yang Z" first="Zhu L" last="Yang">Zhu L. Yang</name><affiliation><nlm:affiliation>Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Zheng" sort="Wang, Zheng" uniqKey="Wang Z" first="Zheng" last="Wang">Zheng Wang</name><affiliation><nlm:affiliation>Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Townsend, Jeffrey P" sort="Townsend, Jeffrey P" uniqKey="Townsend J" first="Jeffrey P" last="Townsend">Jeffrey P. Townsend</name><affiliation><nlm:affiliation>Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Program in Microbiology, Yale University, New Haven, CT 06520, USA.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Environmental microbiology reports</title><idno type="eISSN">1758-2229</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Ascomycota (classification)</term><term>Ascomycota (genetics)</term><term>Ascomycota (isolation & purification)</term><term>Biodiversity (MeSH)</term><term>Biological Evolution (MeSH)</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>Ecosystem (MeSH)</term><term>Mycorrhizae (classification)</term><term>Mycorrhizae (genetics)</term><term>Mycorrhizae (isolation & purification)</term><term>Phylogeny (MeSH)</term><term>Plants (microbiology)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Soil Microbiology (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>Ascomycota</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Ascomycota</term><term>DNA, Fungal</term><term>DNA, Ribosomal Spacer</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Ascomycota</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plants</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biodiversity</term><term>Biological Evolution</term><term>Cluster Analysis</term><term>Ecosystem</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term><term>Soil Microbiology</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The relation between ecological and genetic divergence of Helvella species (saddle fungi) has been perplexing. While a few species have been clearly demonstrated to be ectomycorrhizal fungi, ecological roles of many other species have been controversial, alternately considered as either saprotrophic or mycorrhizal. We applied SATé to build an inclusive deoxyribonucleic acid sequence alignment for the internal transcribed spacers (ITS) of annotated Helvella species and related environmental sequences. Phylogenetic informativeness of ITS and its regions were assessed using PhyDesign. Mycorrhizal lineages present a diversity of ecology, host type and geographic distribution. In two Helvella clades, no Helvella ITS sequences were recovered from root tips. Inclusion of environmental sequences in the ITS phylogeny from these sequences has the potential to link these data and reveal Helvella ecology. This study can serve as a model for revealing the diversity of relationships between unculturable fungi and their potential plant hosts. How non-mycorrhizal life styles within Helvella evolved will require expanded metagenomic investigation of soil and other environmental samples along with study of Helvella genomes. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26033481</PMID><DateCompleted><Year>2016</Year><Month>04</Month><Day>14</Day></DateCompleted><DateRevised><Year>2015</Year><Month>07</Month><Day>22</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1758-2229</ISSN><JournalIssue CitedMedium="Internet"><Volume>7</Volume><Issue>4</Issue><PubDate><Year>2015</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Environmental microbiology reports</Title><ISOAbbreviation>Environ Microbiol Rep</ISOAbbreviation></Journal><ArticleTitle>Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples - an example of saddle fungi.</ArticleTitle><Pagination><MedlinePgn>658-67</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/1758-2229.12303</ELocationID><Abstract><AbstractText>The relation between ecological and genetic divergence of Helvella species (saddle fungi) has been perplexing. While a few species have been clearly demonstrated to be ectomycorrhizal fungi, ecological roles of many other species have been controversial, alternately considered as either saprotrophic or mycorrhizal. We applied SATé to build an inclusive deoxyribonucleic acid sequence alignment for the internal transcribed spacers (ITS) of annotated Helvella species and related environmental sequences. Phylogenetic informativeness of ITS and its regions were assessed using PhyDesign. Mycorrhizal lineages present a diversity of ecology, host type and geographic distribution. In two Helvella clades, no Helvella ITS sequences were recovered from root tips. Inclusion of environmental sequences in the ITS phylogeny from these sequences has the potential to link these data and reveal Helvella ecology. This study can serve as a model for revealing the diversity of relationships between unculturable fungi and their potential plant hosts. How non-mycorrhizal life styles within Helvella evolved will require expanded metagenomic investigation of soil and other environmental samples along with study of Helvella genomes. </AbstractText><CopyrightInformation>© 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hwang</LastName><ForeName>Jonathan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Qi</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Zhu L</ForeName><Initials>ZL</Initials><AffiliationInfo><Affiliation>Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Zheng</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Townsend</LastName><ForeName>Jeffrey P</ForeName><Initials>JP</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-9890-3907</Identifier><AffiliationInfo><Affiliation>Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Program in Microbiology, Yale University, New Haven, CT 06520, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>07</Month><Day>01</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Environ Microbiol Rep</MedlineTA><NlmUniqueID>101499207</NlmUniqueID><ISSNLinking>1758-2229</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004271">DNA, 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