Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi.
Identifieur interne : 001471 ( Main/Exploration ); précédent : 001470; suivant : 001472Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi.
Auteurs : Miranda M. Hart [Canada] ; Kristin Aleklett [Canada] ; Pierre-Luc Chagnon [Canada] ; Cameron Egan [Canada] ; Stefano Ghignone [Italie] ; Thorunn Helgason [Royaume-Uni] ; Ylva Lekberg [États-Unis] ; Maarja Öpik [Estonie] ; Brian J. Pickles [Canada] ; Lauren Waller [États-Unis]Source :
- The New phytologist [ 1469-8137 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Fungal.
- genetics : Biota, Mycorrhizae.
- methods : High-Throughput Nucleotide Sequencing.
- Computational Biology, Databases, Nucleic Acid, Models, Biological, Specimen Handling.
Abstract
Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities.
DOI: 10.1111/nph.13340
PubMed: 25737096
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Hart</name><affiliation wicri:level="1"><nlm:affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Biology University of British Columbia Okanagan, Kelowna, BC</wicri:regionArea><wicri:noRegion>BC</wicri:noRegion></affiliation></author><author><name sortKey="Aleklett, Kristin" sort="Aleklett, Kristin" uniqKey="Aleklett K" first="Kristin" last="Aleklett">Kristin Aleklett</name><affiliation wicri:level="1"><nlm:affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Biology University of British Columbia Okanagan, Kelowna, BC</wicri:regionArea><wicri:noRegion>BC</wicri:noRegion></affiliation></author><author><name sortKey="Chagnon, Pierre Luc" sort="Chagnon, Pierre Luc" uniqKey="Chagnon P" first="Pierre-Luc" last="Chagnon">Pierre-Luc Chagnon</name><affiliation wicri:level="1"><nlm:affiliation>Département de Biologie, Université de Sherbrooke, 2500 Boulevard de l'université, Sherbrooke, QC, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Département de Biologie, Université de Sherbrooke, 2500 Boulevard de l'université, Sherbrooke, QC</wicri:regionArea><wicri:noRegion>QC</wicri:noRegion></affiliation></author><author><name sortKey="Egan, Cameron" sort="Egan, Cameron" uniqKey="Egan C" first="Cameron" last="Egan">Cameron Egan</name><affiliation wicri:level="1"><nlm:affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Biology University of British Columbia Okanagan, Kelowna, BC</wicri:regionArea><wicri:noRegion>BC</wicri:noRegion></affiliation></author><author><name sortKey="Ghignone, Stefano" sort="Ghignone, Stefano" uniqKey="Ghignone S" first="Stefano" last="Ghignone">Stefano Ghignone</name><affiliation wicri:level="3"><nlm:affiliation>Istituto per la Protezione Sostenibile delle Piante (UOS Torino), C.N.R., Torino, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto per la Protezione Sostenibile delle Piante (UOS Torino), C.N.R., Torino</wicri:regionArea><placeName><settlement type="city">Turin</settlement><region type="région" nuts="2">Piémont</region></placeName></affiliation></author><author><name sortKey="Helgason, Thorunn" sort="Helgason, Thorunn" uniqKey="Helgason T" first="Thorunn" last="Helgason">Thorunn Helgason</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, University of York, Heslington, York, YO10 5DD, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Biology, University of York, Heslington, York, YO10 5DD</wicri:regionArea><wicri:noRegion>YO10 5DD</wicri:noRegion></affiliation></author><author><name sortKey="Lekberg, Ylva" sort="Lekberg, Ylva" uniqKey="Lekberg Y" first="Ylva" last="Lekberg">Ylva Lekberg</name><affiliation wicri:level="2"><nlm:affiliation>MPG Ranch and Department for Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>MPG Ranch and Department for Ecosystem and Conservation Sciences, University of Montana, Missoula, MT</wicri:regionArea><placeName><region type="state">Montana</region></placeName></affiliation></author><author><name sortKey="Opik, Maarja" sort="Opik, Maarja" uniqKey="Opik M" first="Maarja" last="Öpik">Maarja Öpik</name><affiliation wicri:level="1"><nlm:affiliation>Department of Botany, University of Tartu, 40 Lai St, 51005, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Botany, University of Tartu, 40 Lai St, 51005, Tartu</wicri:regionArea><wicri:noRegion>Tartu</wicri:noRegion></affiliation></author><author><name sortKey="Pickles, Brian J" sort="Pickles, Brian J" uniqKey="Pickles B" first="Brian J" last="Pickles">Brian J. Pickles</name><affiliation wicri:level="1"><nlm:affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Biology University of British Columbia Okanagan, Kelowna, BC</wicri:regionArea><wicri:noRegion>BC</wicri:noRegion></affiliation></author><author><name sortKey="Waller, Lauren" sort="Waller, Lauren" uniqKey="Waller L" first="Lauren" last="Waller">Lauren Waller</name><affiliation wicri:level="2"><nlm:affiliation>Division of Biological Sciences, University of Montana, Missoula, MT, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Biological Sciences, University of Montana, Missoula, MT</wicri:regionArea><placeName><region type="state">Montana</region></placeName></affiliation></author></analytic><series><title level="j">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biota (genetics)</term><term>Computational Biology (MeSH)</term><term>DNA, Fungal (genetics)</term><term>Databases, Nucleic Acid (MeSH)</term><term>High-Throughput Nucleotide Sequencing (methods)</term><term>Models, Biological (MeSH)</term><term>Mycorrhizae (genetics)</term><term>Specimen Handling (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN fongique (génétique)</term><term>Bases de données d'acides nucléiques (MeSH)</term><term>Biologie informatique (MeSH)</term><term>Biote (génétique)</term><term>Manipulation d'échantillons (MeSH)</term><term>Modèles biologiques (MeSH)</term><term>Mycorhizes (génétique)</term><term>Séquençage nucléotidique à haut débit (méthodes)</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>Biota</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN fongique</term><term>Biote</term><term>Mycorhizes</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Séquençage nucléotidique à haut débit</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computational Biology</term><term>Databases, Nucleic Acid</term><term>Models, Biological</term><term>Specimen Handling</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données d'acides nucléiques</term><term>Biologie informatique</term><term>Manipulation d'échantillons</term><term>Modèles biologiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25737096</PMID><DateCompleted><Year>2016</Year><Month>04</Month><Day>08</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1469-8137</ISSN><JournalIssue CitedMedium="Internet"><Volume>207</Volume><Issue>1</Issue><PubDate><Year>2015</Year><Month>Jul</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi.</ArticleTitle><Pagination><MedlinePgn>235-47</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.13340</ELocationID><Abstract><AbstractText>Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities. </AbstractText><CopyrightInformation>© 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hart</LastName><ForeName>Miranda M</ForeName><Initials>MM</Initials><AffiliationInfo><Affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Aleklett</LastName><ForeName>Kristin</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chagnon</LastName><ForeName>Pierre-Luc</ForeName><Initials>PL</Initials><AffiliationInfo><Affiliation>Département de Biologie, Université de Sherbrooke, 2500 Boulevard de l'université, Sherbrooke, QC, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Egan</LastName><ForeName>Cameron</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ghignone</LastName><ForeName>Stefano</ForeName><Initials>S</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-2033-2286</Identifier><AffiliationInfo><Affiliation>Istituto per la Protezione Sostenibile delle Piante (UOS Torino), C.N.R., Torino, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Helgason</LastName><ForeName>Thorunn</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Biology, University of York, Heslington, York, YO10 5DD, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lekberg</LastName><ForeName>Ylva</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>MPG Ranch and Department for Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Öpik</LastName><ForeName>Maarja</ForeName><Initials>M</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-8025-7460</Identifier><AffiliationInfo><Affiliation>Department of Botany, University of Tartu, 40 Lai St, 51005, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pickles</LastName><ForeName>Brian J</ForeName><Initials>BJ</Initials><AffiliationInfo><Affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Waller</LastName><ForeName>Lauren</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Division of Biological Sciences, University of Montana, Missoula, MT, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>BB/L026007/1</GrantID><Agency>Biotechnology and Biological Sciences Research Council</Agency><Country>United Kingdom</Country></Grant></GrantList><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>03</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>New Phytol</MedlineTA><NlmUniqueID>9882884</NlmUniqueID><ISSNLinking>0028-646X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004271">DNA, Fungal</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D058448" MajorTopicYN="N">Biota</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004271" MajorTopicYN="N">DNA, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D030561" MajorTopicYN="N">Databases, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008954" MajorTopicYN="N">Models, Biological</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013048" MajorTopicYN="N">Specimen Handling</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">PCR</Keyword><Keyword MajorTopicYN="N">arbuscular mycorrhizal fungi (AMF)</Keyword><Keyword MajorTopicYN="N">bioinformatics</Keyword><Keyword MajorTopicYN="N">environmental sequencing</Keyword><Keyword MajorTopicYN="N">next generation sequencing (NGS)</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>10</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>01</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>3</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>3</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>4</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25737096</ArticleId><ArticleId 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HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:25737096" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MycorrhizaeV1
| This area was generated with Dilib version V0.6.37. |  |