Sequence-based classification and identification of Fungi

TY - JOUR

T1 - Sequence-based classification and identification of Fungi

AU - Hibbett, David

AU - Abarenkov, Kessy

AU - Koljalg, Urmas

AU - Opik, Maarja

AU - Chai, Benli

AU - Cole, James R.

AU - Wang, Qiong

AU - Crous, Pedro W.

AU - Robert, Vincent A. R. G.

AU - Helgason, Thorunn

AU - Herr, Josh

AU - Kirk, Paul

AU - Lueschow, Shiloh

AU - O'Donnell, Kerry

AU - Nilsson, Henrik

AU - Oono, Ryoko

AU - Schoch, Conrad L.

AU - Smyth, Christopher

AU - Walker, Donny

AU - Porras-Alfaro, Andrea

AU - Taylor, John W.

AU - Geiser, David M.

N1 - © 2016, Mycologia. This is an author-produced version of the published paper. Uploaded in accordance with the publisher’s self-archiving policy. Further copying may not be permitted; contact the publisher for details

PY - 2017/1/30

Y1 - 2017/1/30

N2 - Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable valid publication of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.

AB - Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable valid publication of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.

M3 - Article

SN - 0027-5514

VL - 108

SP - 1049

EP - 1068

JO - Mycologia

JF - Mycologia

IS - 6

ER -