Journal
NEW PHYTOLOGIST
Volume 207, Issue 1, Pages 235-247Publisher
WILEY
DOI: 10.1111/nph.13340
Keywords
arbuscular mycorrhizal fungi (AMF); bioinformatics; environmental sequencing; next generation sequencing (NGS); PCR
Categories
Funding
- University of British Columbia Okanagan
- RISINNOVA Project [2010-2369]
- PURE [FP7-265865]
- European Community
- ECOFLOR, Piemonte Region
- MPG Ranch
- Estonian Science Foundation [9050, IUT20-28]
- European Regional Development Fund (Center of Excellence FIBIR)
- Natural Environment Research Council (NERC) [NE/M004864/1]
- Biotechnology and Biosciences Research Council (BBSRC) [BB/L026007/1]
- Simard lab at UBC Vancouver
- Mohn lab at UBC Vancouver
- AGER Foundation
- BBSRC [BB/L026007/1] Funding Source: UKRI
- NERC [NE/M004864/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/L026007/1] Funding Source: researchfish
- Natural Environment Research Council [NE/M004864/1] Funding Source: researchfish
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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.
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