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Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide

Lindahl, Björn and Nilsson, Henrik and Tedersoo, Leho and Abarenkov, Kessy and Carlsen, Tor and Kjøller, Rasmus and Kõljalg, Urmas and Pennanen, Taina and Rosendahl, Søren and Stenlid, Jan and Kauserud, Håvard (2013). Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide. New phytologist. 199:1, 288-299
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Official URL: http://dx.doi.org/10.1111/nph.12243

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.

Authors/Creators:Lindahl, Björn and Nilsson, Henrik and Tedersoo, Leho and Abarenkov, Kessy and Carlsen, Tor and Kjøller, Rasmus and Kõljalg, Urmas and Pennanen, Taina and Rosendahl, Søren and Stenlid, Jan and Kauserud, Håvard
Title:Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide
Series/Journal:New phytologist (1469-8137)
Year of publishing :2013
Volume:199
Number:1
Page range:288-299
Number of Pages:12
Publisher:Wiley, New Phytologist Trust
ISSN:1469-8137
Language:English
Additional Information:Wiley Online Open
Publication Type:Journal article
Refereed:Yes
Article category:Scientific peer reviewed
Version:Published version
Full Text Status:Public
Agris subject categories.:F Plant production > F40 Plant ecology
X Agricola extesions > X30 Life sciences
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Biochemistry and Molecular Biology
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Microbiology (Microbiology in the medical area to be 30109)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Bioinformatics and Systems Biology (methods development to be 10203)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Ecology
Agrovoc terms:bioinformatics, PCR
Keywords:454-pyrosequencing, bioinformatics, barcoding, environmental sequencing, internal transcribed spacer (ITS) region, PCR
URN:NBN:urn:nbn:se:slu:epsilon-e-1848
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-1848
Additional ID:
Type of IDID
Web of Science (WoS)000319520200028
DOI10.1111/nph.12243
ID Code:11044
Faculty:S - Faculty of Forest Sciences
Department:(NL, NJ) > Dept. of Forest Mycology and Plant Pathology
(S) > Dept. of Forest Mycology and Plant Pathology
Deposited By: SLUpub Connector
Deposited On:07 Apr 2014 13:01
Metadata Last Modified:14 Apr 2015 09:46

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