Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi.
Identifieur interne : 001528 ( Main/Corpus ); précédent : 001527; suivant : 001529Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi.
Auteurs : Miranda M. Hart ; Kristin Aleklett ; Pierre-Luc Chagnon ; Cameron Egan ; Stefano Ghignone ; Thorunn Helgason ; Ylva Lekberg ; Maarja Öpik ; Brian J. Pickles ; Lauren WallerSource :
- The New phytologist [ 1469-8137 ] ; 2015.
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
Links to Exploration step
pubmed:25737096Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi.</title><author><name sortKey="Hart, Miranda M" sort="Hart, Miranda M" uniqKey="Hart M" first="Miranda M" last="Hart">Miranda M. Hart</name><affiliation><nlm:affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Aleklett, Kristin" sort="Aleklett, Kristin" uniqKey="Aleklett K" first="Kristin" last="Aleklett">Kristin Aleklett</name><affiliation><nlm:affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</nlm:affiliation></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><nlm:affiliation>Département de Biologie, Université de Sherbrooke, 2500 Boulevard de l'université, Sherbrooke, QC, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Egan, Cameron" sort="Egan, Cameron" uniqKey="Egan C" first="Cameron" last="Egan">Cameron Egan</name><affiliation><nlm:affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Ghignone, Stefano" sort="Ghignone, Stefano" uniqKey="Ghignone S" first="Stefano" last="Ghignone">Stefano Ghignone</name><affiliation><nlm:affiliation>Istituto per la Protezione Sostenibile delle Piante (UOS Torino), C.N.R., Torino, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Helgason, Thorunn" sort="Helgason, Thorunn" uniqKey="Helgason T" first="Thorunn" last="Helgason">Thorunn Helgason</name><affiliation><nlm:affiliation>Department of Biology, University of York, Heslington, York, YO10 5DD, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Lekberg, Ylva" sort="Lekberg, Ylva" uniqKey="Lekberg Y" first="Ylva" last="Lekberg">Ylva Lekberg</name><affiliation><nlm:affiliation>MPG Ranch and Department for Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Opik, Maarja" sort="Opik, Maarja" uniqKey="Opik M" first="Maarja" last="Öpik">Maarja Öpik</name><affiliation><nlm:affiliation>Department of Botany, University of Tartu, 40 Lai St, 51005, Tartu, Estonia.</nlm:affiliation></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><nlm:affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Waller, Lauren" sort="Waller, Lauren" uniqKey="Waller L" first="Lauren" last="Waller">Lauren Waller</name><affiliation><nlm:affiliation>Division of Biological Sciences, University of Montana, Missoula, MT, USA.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:25737096</idno><idno type="pmid">25737096</idno><idno type="doi">10.1111/nph.13340</idno><idno type="wicri:Area/Main/Corpus">001528</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001528</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi.</title><author><name sortKey="Hart, Miranda M" sort="Hart, Miranda M" uniqKey="Hart M" first="Miranda M" last="Hart">Miranda M. Hart</name><affiliation><nlm:affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Aleklett, Kristin" sort="Aleklett, Kristin" uniqKey="Aleklett K" first="Kristin" last="Aleklett">Kristin Aleklett</name><affiliation><nlm:affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</nlm:affiliation></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><nlm:affiliation>Département de Biologie, Université de Sherbrooke, 2500 Boulevard de l'université, Sherbrooke, QC, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Egan, Cameron" sort="Egan, Cameron" uniqKey="Egan C" first="Cameron" last="Egan">Cameron Egan</name><affiliation><nlm:affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Ghignone, Stefano" sort="Ghignone, Stefano" uniqKey="Ghignone S" first="Stefano" last="Ghignone">Stefano Ghignone</name><affiliation><nlm:affiliation>Istituto per la Protezione Sostenibile delle Piante (UOS Torino), C.N.R., Torino, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Helgason, Thorunn" sort="Helgason, Thorunn" uniqKey="Helgason T" first="Thorunn" last="Helgason">Thorunn Helgason</name><affiliation><nlm:affiliation>Department of Biology, University of York, Heslington, York, YO10 5DD, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Lekberg, Ylva" sort="Lekberg, Ylva" uniqKey="Lekberg Y" first="Ylva" last="Lekberg">Ylva Lekberg</name><affiliation><nlm:affiliation>MPG Ranch and Department for Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Opik, Maarja" sort="Opik, Maarja" uniqKey="Opik M" first="Maarja" last="Öpik">Maarja Öpik</name><affiliation><nlm:affiliation>Department of Botany, University of Tartu, 40 Lai St, 51005, Tartu, Estonia.</nlm:affiliation></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><nlm:affiliation>Biology University of British Columbia Okanagan, Kelowna, BC, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Waller, Lauren" sort="Waller, Lauren" uniqKey="Waller L" first="Lauren" last="Waller">Lauren Waller</name><affiliation><nlm:affiliation>Division of Biological Sciences, University of Montana, Missoula, MT, USA.</nlm:affiliation></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="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="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</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></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 IdType="doi">10.1111/nph.13340</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/MycorrhizaeV1/Data/Main/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001528 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Corpus/biblio.hfd -nk 001528 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= MycorrhizaeV1
|flux= Main
|étape= Corpus
|type= RBID
|clé= pubmed:25737096
|texte= Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Corpus/RBID.i -Sk "pubmed:25737096" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Corpus/biblio.hfd \
| NlmPubMed2Wicri -a MycorrhizaeV1
| This area was generated with Dilib version V0.6.37. |  |