Fungal community analysis by high‐throughput sequencing of amplified markers – a user's guide
Citations Over TimeTop 1% of 2013 papers
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.
Related Papers
- → EFFECT OF THE NEMATODE PHASMARHABDITIS HERMAPHRODITA ON YOUNGSTAGES OF THE PEST SLUG ARION LUSITANICUS(2002)40 cited
- → Cloning and Characterization of Rat BAT3 cDNA(1999)20 cited
- → HLA-B-associated transcript 3 (Bat3)/Scythe is essential for p300-mediated acetylation of p53(2007)127 cited
- → DETERMINING QUALITY REQUIREMENTS AT THE UNIVERSITIES TO IMPROVE THE QUALITY OF EDUCATION(2018)
- → ИСПОЛЬЗОВAНИЕ ПОТЕНЦИAЛA СОЦИAЛЬНЫХ ПAРТНЕРОВ В ПОДГОТОВКЕ БУДУЩИХ ПЕДAГОГОВ(2024)