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

New Phytologist - Tập 199 Số 1 - Trang 288-299 - 2013
Björn D. Lindahl1, R. Henrik Nilsson2, Leho Tedersoo3, Kessy Abarenkov3, Tor Carlsen4, Rasmus Kjøller5, Urmas Kõljalg3, Taina Pennanen6, Søren Rosendahl5, Jan Stenlid1, Håvard Kauserud4
1Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07 Uppsala, Sweden
2Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Gothenburg, Sweden
3Institute of Ecology and Earth Sciences/Natural History Museum University of Tartu 46 Vanemuise St. 51014 Tartu Estonia
4Department of Biology, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
5Department of Biology University of Copenhagen Øster Farimagsgade 2D 1353 Copenhagen Denmark
6The Finnish Forest Research Institute, PL 18, FI-01301 Vantaa, Finland

Tóm tắt

Summary 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.

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New Phytologist

Tập 199 Số 1

288-299

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