Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide
Novel high-throughput sequencing methods outperform earlier approaches in terms of resolution and magnitude. They enable identification and relative quantification of community members and offer new insights into fungal community ecology. These methods are currently taking over as the primary tool t...
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creator | Lindahl, Björn D. Nilsson, R. Henrik Tedersoo, Leho Abarenkov, Kessy Carlsen, Tor Kjøller, Rasmus Kõljalg, Urmas Pennanen, Taina Rosendahl, Søren Stenlid, Jan Kauserud, Håvard |
description | Novel high-throughput sequencing methods outperform earlier approaches in terms of resolution and magnitude. They enable identification and relative quantification of community members and offer new insights into fungal community ecology. These methods are currently taking over as the primary tool to assess fungal communities of plant-associated endophytes, pathogens, and mycorrhizal symbionts, as well as free-living saprotrophs.
Taking advantage of the collective experience of six research groups, we here review the different stages involved in fungal community analysis, from field sampling via laboratory procedures to bioinformatics and data interpretation. We discuss potential pitfalls, alternatives, and solutions.
Highlighted topics are challenges involved in: obtaining representative DNA/RNA samples and replicates that encompass the targeted variation in community composition, selection of marker regions and primers, options for amplification and multiplexing, handling of sequencing errors, and taxonomic identification.
Without awareness of methodological biases, limitations of markers, and bioinformatics challenges, large-scale sequencing projects risk yielding artificial results and misleading conclusions. |
doi_str_mv | 10.1111/nph.12243 |
format | Article |
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Taking advantage of the collective experience of six research groups, we here review the different stages involved in fungal community analysis, from field sampling via laboratory procedures to bioinformatics and data interpretation. We discuss potential pitfalls, alternatives, and solutions.
Highlighted topics are challenges involved in: obtaining representative DNA/RNA samples and replicates that encompass the targeted variation in community composition, selection of marker regions and primers, options for amplification and multiplexing, handling of sequencing errors, and taxonomic identification.
Without awareness of methodological biases, limitations of markers, and bioinformatics challenges, large-scale sequencing projects risk yielding artificial results and misleading conclusions.</description><identifier>ISSN: 0028-646X</identifier><identifier>ISSN: 1469-8137</identifier><identifier>EISSN: 1469-8137</identifier><identifier>DOI: 10.1111/nph.12243</identifier><identifier>PMID: 23534863</identifier><language>eng</language><publisher>England: New Phytologist Trust</publisher><subject>454‐pyrosequencing ; Amplification ; barcoding ; Biochemistry and Molecular Biology ; Bioinformatics ; Bioinformatics and Systems Biology ; Bioinformatik och systembiologi ; Biokemi och molekylärbiologi ; Biological Systematics ; Biologisk systematik ; Biomarkers ; Biota ; Botanik ; Botany ; Community composition ; Community involvement ; Computational Biology - methods ; Data interpretation ; Deoxyribonucleic acid ; DNA ; DNA Primers ; DNA, Fungal - analysis ; DNA, Intergenic ; Ecology ; Ekologi ; Endophytes ; environmental sequencing ; Forest soils ; Fungi ; Fungi - classification ; Fungi - genetics ; Genetic Markers ; High-Throughput Nucleotide Sequencing - methods ; Identification ; internal transcribed spacer (ITS) region ; Manuals ; Markvetenskap ; Metagenomics ; Methods ; Microbiology ; Microbiology in the medical area ; Mikrobiologi ; Mikrobiologi inom det medicinska området ; Multiplexing ; Mycorrhizae - genetics ; Pathogens ; PCR ; Phylogenetics ; Plant communities ; Polymerase chain reaction ; Polymerase Chain Reaction - methods ; Primers ; Product category rules ; Sequencing ; Soil Microbiology ; Soil Science ; Symbionts ; Synecology</subject><ispartof>The New phytologist, 2013-07, Vol.199 (1), p.288-299</ispartof><rights>2013 New Phytologist Trust</rights><rights>2013 The Authors. New Phytologist © 2013 New Phytologist Trust</rights><rights>2013 The Authors. New Phytologist © 2013 New Phytologist Trust.</rights><rights>Copyright © 2013 New Phytologist Trust</rights><rights>Copyright © 2013 New Phytologist Trust 2013</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c6843-c9c986b61eacdb865207a99d46740d128cfa37d1d87a4f81ede0d3dd02dcbbfe3</citedby><cites>FETCH-LOGICAL-c6843-c9c986b61eacdb865207a99d46740d128cfa37d1d87a4f81ede0d3dd02dcbbfe3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/newphytologist.199.1.288$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/newphytologist.199.1.288$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,552,780,784,803,885,1417,1433,27924,27925,45574,45575,46409,46833,58017,58250</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23534863$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://gup.ub.gu.se/publication/175522$$DView record from Swedish Publication Index$$Hfree_for_read</backlink><backlink>$$Uhttps://res.slu.se/id/publ/52078$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Lindahl, Björn D.</creatorcontrib><creatorcontrib>Nilsson, R. Henrik</creatorcontrib><creatorcontrib>Tedersoo, Leho</creatorcontrib><creatorcontrib>Abarenkov, Kessy</creatorcontrib><creatorcontrib>Carlsen, Tor</creatorcontrib><creatorcontrib>Kjøller, Rasmus</creatorcontrib><creatorcontrib>Kõljalg, Urmas</creatorcontrib><creatorcontrib>Pennanen, Taina</creatorcontrib><creatorcontrib>Rosendahl, Søren</creatorcontrib><creatorcontrib>Stenlid, Jan</creatorcontrib><creatorcontrib>Kauserud, Håvard</creatorcontrib><creatorcontrib>Sveriges lantbruksuniversitet</creatorcontrib><title>Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide</title><title>The New phytologist</title><addtitle>New Phytol</addtitle><description>Novel high-throughput sequencing methods outperform earlier approaches in terms of resolution and magnitude. They enable identification and relative quantification of community members and offer new insights into fungal community ecology. These methods are currently taking over as the primary tool to assess fungal communities of plant-associated endophytes, pathogens, and mycorrhizal symbionts, as well as free-living saprotrophs.
Taking advantage of the collective experience of six research groups, we here review the different stages involved in fungal community analysis, from field sampling via laboratory procedures to bioinformatics and data interpretation. We discuss potential pitfalls, alternatives, and solutions.
Highlighted topics are challenges involved in: obtaining representative DNA/RNA samples and replicates that encompass the targeted variation in community composition, selection of marker regions and primers, options for amplification and multiplexing, handling of sequencing errors, and taxonomic identification.
Without awareness of methodological biases, limitations of markers, and bioinformatics challenges, large-scale sequencing projects risk yielding artificial results and misleading conclusions.</description><subject>454‐pyrosequencing</subject><subject>Amplification</subject><subject>barcoding</subject><subject>Biochemistry and Molecular Biology</subject><subject>Bioinformatics</subject><subject>Bioinformatics and Systems Biology</subject><subject>Bioinformatik och systembiologi</subject><subject>Biokemi och molekylärbiologi</subject><subject>Biological Systematics</subject><subject>Biologisk systematik</subject><subject>Biomarkers</subject><subject>Biota</subject><subject>Botanik</subject><subject>Botany</subject><subject>Community composition</subject><subject>Community involvement</subject><subject>Computational Biology - methods</subject><subject>Data interpretation</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA Primers</subject><subject>DNA, Fungal - analysis</subject><subject>DNA, Intergenic</subject><subject>Ecology</subject><subject>Ekologi</subject><subject>Endophytes</subject><subject>environmental sequencing</subject><subject>Forest soils</subject><subject>Fungi</subject><subject>Fungi - classification</subject><subject>Fungi - genetics</subject><subject>Genetic Markers</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Identification</subject><subject>internal transcribed spacer (ITS) region</subject><subject>Manuals</subject><subject>Markvetenskap</subject><subject>Metagenomics</subject><subject>Methods</subject><subject>Microbiology</subject><subject>Microbiology in the medical area</subject><subject>Mikrobiologi</subject><subject>Mikrobiologi inom det medicinska området</subject><subject>Multiplexing</subject><subject>Mycorrhizae - genetics</subject><subject>Pathogens</subject><subject>PCR</subject><subject>Phylogenetics</subject><subject>Plant communities</subject><subject>Polymerase chain reaction</subject><subject>Polymerase Chain Reaction - methods</subject><subject>Primers</subject><subject>Product category rules</subject><subject>Sequencing</subject><subject>Soil Microbiology</subject><subject>Soil Science</subject><subject>Symbionts</subject><subject>Synecology</subject><issn>0028-646X</issn><issn>1469-8137</issn><issn>1469-8137</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>WIN</sourceid><sourceid>EIF</sourceid><sourceid>D8T</sourceid><recordid>eNqNkstu1DAUhiMEokNhwQsgSyyARVrf4tgbJFRRilQBC5DYWU7sJB6SOLVjRtnxDrwhT4KnMx1RJCq8OZLPd36dy59lTxE8QemdjlN3gjCm5F62QpSJnCNS3s9WEGKeM8q-HmWPQlhDCEXB8MPsCJOCUM7IKpPncWxVD2o3DHG08wLUqPol2ACqBXS27fK58y623RRnEMxVNGNtxxa4Bqhh6m1jjQaD8t-MD-DXj59AgRiMfxFAG602j7MHjeqDebKPx9mX87efzy7yy4_v3p-9ucxrxinJa1ELziqGjKp1xVmBYamE0JSVFGqEed0oUmqkealow5HRBmqiNcS6rqrGkOMs3-mGjZliJSdvU1OLdMrK0MdK-W2QwcitNL-Tb-Mk01d7jaOyKDBO_Osdn-DB6NqMs1f9rbLbmdF2snXfJSkRpmWZBF7uBbxLSwyzHGyoTd-r0bgYJCJCCJgGL_4DLZgo0mJIQp__ha5d9OmCQeICEcIJL-ldFKIEEwwx2VKvdlTtXQjeNIfpEJRbn8nkM3nts8Q--3MdB_LGWAk43QEb25vl30ryw6eLG8n9RdZhdv5QMZrN1C2z611rU-NICIkk5pz8BmHI8Bo</recordid><startdate>201307</startdate><enddate>201307</enddate><creator>Lindahl, Björn D.</creator><creator>Nilsson, R. Henrik</creator><creator>Tedersoo, Leho</creator><creator>Abarenkov, Kessy</creator><creator>Carlsen, Tor</creator><creator>Kjøller, Rasmus</creator><creator>Kõljalg, Urmas</creator><creator>Pennanen, Taina</creator><creator>Rosendahl, Søren</creator><creator>Stenlid, Jan</creator><creator>Kauserud, Håvard</creator><general>New Phytologist Trust</general><general>Wiley Subscription Services, Inc</general><general>Blackwell Publishing Ltd</general><scope>24P</scope><scope>WIN</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7SN</scope><scope>8FD</scope><scope>C1K</scope><scope>F1W</scope><scope>FR3</scope><scope>H95</scope><scope>L.G</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>ADTPV</scope><scope>AOWAS</scope><scope>F1U</scope><scope>D8T</scope><scope>ZZAVC</scope></search><sort><creationdate>201307</creationdate><title>Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide</title><author>Lindahl, Björn D. ; Nilsson, R. Henrik ; Tedersoo, Leho ; Abarenkov, Kessy ; Carlsen, Tor ; Kjøller, Rasmus ; Kõljalg, Urmas ; Pennanen, Taina ; Rosendahl, Søren ; Stenlid, Jan ; Kauserud, Håvard</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c6843-c9c986b61eacdb865207a99d46740d128cfa37d1d87a4f81ede0d3dd02dcbbfe3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>454‐pyrosequencing</topic><topic>Amplification</topic><topic>barcoding</topic><topic>Biochemistry and Molecular Biology</topic><topic>Bioinformatics</topic><topic>Bioinformatics and Systems Biology</topic><topic>Bioinformatik och systembiologi</topic><topic>Biokemi och molekylärbiologi</topic><topic>Biological Systematics</topic><topic>Biologisk systematik</topic><topic>Biomarkers</topic><topic>Biota</topic><topic>Botanik</topic><topic>Botany</topic><topic>Community composition</topic><topic>Community involvement</topic><topic>Computational Biology - methods</topic><topic>Data interpretation</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA Primers</topic><topic>DNA, Fungal - analysis</topic><topic>DNA, Intergenic</topic><topic>Ecology</topic><topic>Ekologi</topic><topic>Endophytes</topic><topic>environmental sequencing</topic><topic>Forest soils</topic><topic>Fungi</topic><topic>Fungi - classification</topic><topic>Fungi - genetics</topic><topic>Genetic Markers</topic><topic>High-Throughput Nucleotide Sequencing - methods</topic><topic>Identification</topic><topic>internal transcribed spacer (ITS) region</topic><topic>Manuals</topic><topic>Markvetenskap</topic><topic>Metagenomics</topic><topic>Methods</topic><topic>Microbiology</topic><topic>Microbiology in the medical area</topic><topic>Mikrobiologi</topic><topic>Mikrobiologi inom det medicinska området</topic><topic>Multiplexing</topic><topic>Mycorrhizae - genetics</topic><topic>Pathogens</topic><topic>PCR</topic><topic>Phylogenetics</topic><topic>Plant communities</topic><topic>Polymerase chain reaction</topic><topic>Polymerase Chain Reaction - methods</topic><topic>Primers</topic><topic>Product category rules</topic><topic>Sequencing</topic><topic>Soil Microbiology</topic><topic>Soil Science</topic><topic>Symbionts</topic><topic>Synecology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lindahl, Björn D.</creatorcontrib><creatorcontrib>Nilsson, R. 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Henrik</au><au>Tedersoo, Leho</au><au>Abarenkov, Kessy</au><au>Carlsen, Tor</au><au>Kjøller, Rasmus</au><au>Kõljalg, Urmas</au><au>Pennanen, Taina</au><au>Rosendahl, Søren</au><au>Stenlid, Jan</au><au>Kauserud, Håvard</au><aucorp>Sveriges lantbruksuniversitet</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide</atitle><jtitle>The New phytologist</jtitle><addtitle>New Phytol</addtitle><date>2013-07</date><risdate>2013</risdate><volume>199</volume><issue>1</issue><spage>288</spage><epage>299</epage><pages>288-299</pages><issn>0028-646X</issn><issn>1469-8137</issn><eissn>1469-8137</eissn><abstract>Novel high-throughput sequencing methods outperform earlier approaches in terms of resolution and magnitude. They enable identification and relative quantification of community members and offer new insights into fungal community ecology. These methods are currently taking over as the primary tool to assess fungal communities of plant-associated endophytes, pathogens, and mycorrhizal symbionts, as well as free-living saprotrophs.
Taking advantage of the collective experience of six research groups, we here review the different stages involved in fungal community analysis, from field sampling via laboratory procedures to bioinformatics and data interpretation. We discuss potential pitfalls, alternatives, and solutions.
Highlighted topics are challenges involved in: obtaining representative DNA/RNA samples and replicates that encompass the targeted variation in community composition, selection of marker regions and primers, options for amplification and multiplexing, handling of sequencing errors, and taxonomic identification.
Without awareness of methodological biases, limitations of markers, and bioinformatics challenges, large-scale sequencing projects risk yielding artificial results and misleading conclusions.</abstract><cop>England</cop><pub>New Phytologist Trust</pub><pmid>23534863</pmid><doi>10.1111/nph.12243</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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subjects | 454‐pyrosequencing Amplification barcoding Biochemistry and Molecular Biology Bioinformatics Bioinformatics and Systems Biology Bioinformatik och systembiologi Biokemi och molekylärbiologi Biological Systematics Biologisk systematik Biomarkers Biota Botanik Botany Community composition Community involvement Computational Biology - methods Data interpretation Deoxyribonucleic acid DNA DNA Primers DNA, Fungal - analysis DNA, Intergenic Ecology Ekologi Endophytes environmental sequencing Forest soils Fungi Fungi - classification Fungi - genetics Genetic Markers High-Throughput Nucleotide Sequencing - methods Identification internal transcribed spacer (ITS) region Manuals Markvetenskap Metagenomics Methods Microbiology Microbiology in the medical area Mikrobiologi Mikrobiologi inom det medicinska området Multiplexing Mycorrhizae - genetics Pathogens PCR Phylogenetics Plant communities Polymerase chain reaction Polymerase Chain Reaction - methods Primers Product category rules Sequencing Soil Microbiology Soil Science Symbionts Synecology |
title | Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide |
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