Sequence-based classification and identification of Fungi

David Hibbett, Kessy Abarenkov, Urmas Kõljalg, Maarja Öpik, Benli Chai, James Cole, Qiong Wang, Pedro Crous, Vincent Robert, Thorunn Helgason, Joshua R. Herr, Paul Kirk, Shiloh Lueschow, Kerry O'Donnell, R. Henrik Nilsson, Ryoko Oono, Conrad Schoch, Christopher Smyth, Donald M. Walker, Andrea Porras-Alfaro & 2 others John W. Taylor, David Michael Geiser

Research output: Contribution to journalReview article

56 Citations (Scopus)

Abstract

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 validPUBLICation 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.

Original languageEnglish (US)
Pages (from-to)1049-1068
Number of pages20
JournalMycologia
Volume108
Issue number6
DOIs
StatePublished - Nov 1 2016

Fingerprint

Fungi
fungus
taxonomy
fungi
Metagenomics
metadata
prokaryote
resource
data quality
accessibility
genomics
Workflow
ecology
fungal communities
Firearms
credit
prokaryotic cells
Genomics
ecologists
Ecology

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Physiology
  • Molecular Biology
  • Genetics
  • Cell Biology

Cite this

Hibbett, D., Abarenkov, K., Kõljalg, U., Öpik, M., Chai, B., Cole, J., ... Geiser, D. M. (2016). Sequence-based classification and identification of Fungi. Mycologia, 108(6), 1049-1068. https://doi.org/10.3852/16-130
Hibbett, David ; Abarenkov, Kessy ; Kõljalg, Urmas ; Öpik, Maarja ; Chai, Benli ; Cole, James ; Wang, Qiong ; Crous, Pedro ; Robert, Vincent ; Helgason, Thorunn ; Herr, Joshua R. ; Kirk, Paul ; Lueschow, Shiloh ; O'Donnell, Kerry ; Nilsson, R. Henrik ; Oono, Ryoko ; Schoch, Conrad ; Smyth, Christopher ; Walker, Donald M. ; Porras-Alfaro, Andrea ; Taylor, John W. ; Geiser, David Michael. / Sequence-based classification and identification of Fungi. In: Mycologia. 2016 ; Vol. 108, No. 6. pp. 1049-1068.
@article{18c2414ea0094dca9776b7ade1fcf694,
title = "Sequence-based classification and identification of Fungi",
abstract = "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 validPUBLICation 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.",
author = "David Hibbett and Kessy Abarenkov and Urmas K{\~o}ljalg and Maarja {\"O}pik and Benli Chai and James Cole and Qiong Wang and Pedro Crous and Vincent Robert and Thorunn Helgason and Herr, {Joshua R.} and Paul Kirk and Shiloh Lueschow and Kerry O'Donnell and Nilsson, {R. Henrik} and Ryoko Oono and Conrad Schoch and Christopher Smyth and Walker, {Donald M.} and Andrea Porras-Alfaro and Taylor, {John W.} and Geiser, {David Michael}",
year = "2016",
month = "11",
day = "1",
doi = "10.3852/16-130",
language = "English (US)",
volume = "108",
pages = "1049--1068",
journal = "Mycologia",
issn = "0027-5514",
publisher = "Allen Press Inc.",
number = "6",

}

Hibbett, D, Abarenkov, K, Kõljalg, U, Öpik, M, Chai, B, Cole, J, Wang, Q, Crous, P, Robert, V, Helgason, T, Herr, JR, Kirk, P, Lueschow, S, O'Donnell, K, Nilsson, RH, Oono, R, Schoch, C, Smyth, C, Walker, DM, Porras-Alfaro, A, Taylor, JW & Geiser, DM 2016, 'Sequence-based classification and identification of Fungi', Mycologia, vol. 108, no. 6, pp. 1049-1068. https://doi.org/10.3852/16-130

Sequence-based classification and identification of Fungi. / Hibbett, David; Abarenkov, Kessy; Kõljalg, Urmas; Öpik, Maarja; Chai, Benli; Cole, James; Wang, Qiong; Crous, Pedro; Robert, Vincent; Helgason, Thorunn; Herr, Joshua R.; Kirk, Paul; Lueschow, Shiloh; O'Donnell, Kerry; Nilsson, R. Henrik; Oono, Ryoko; Schoch, Conrad; Smyth, Christopher; Walker, Donald M.; Porras-Alfaro, Andrea; Taylor, John W.; Geiser, David Michael.

In: Mycologia, Vol. 108, No. 6, 01.11.2016, p. 1049-1068.

Research output: Contribution to journalReview article

TY - JOUR

T1 - Sequence-based classification and identification of Fungi

AU - Hibbett, David

AU - Abarenkov, Kessy

AU - Kõljalg, Urmas

AU - Öpik, Maarja

AU - Chai, Benli

AU - Cole, James

AU - Wang, Qiong

AU - Crous, Pedro

AU - Robert, Vincent

AU - Helgason, Thorunn

AU - Herr, Joshua R.

AU - Kirk, Paul

AU - Lueschow, Shiloh

AU - O'Donnell, Kerry

AU - Nilsson, R. Henrik

AU - Oono, Ryoko

AU - Schoch, Conrad

AU - Smyth, Christopher

AU - Walker, Donald M.

AU - Porras-Alfaro, Andrea

AU - Taylor, John W.

AU - Geiser, David Michael

PY - 2016/11/1

Y1 - 2016/11/1

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 validPUBLICation 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 validPUBLICation 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.

UR - http://www.scopus.com/inward/record.url?scp=85017041359&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85017041359&partnerID=8YFLogxK

U2 - 10.3852/16-130

DO - 10.3852/16-130

M3 - Review article

VL - 108

SP - 1049

EP - 1068

JO - Mycologia

JF - Mycologia

SN - 0027-5514

IS - 6

ER -

Hibbett D, Abarenkov K, Kõljalg U, Öpik M, Chai B, Cole J et al. Sequence-based classification and identification of Fungi. Mycologia. 2016 Nov 1;108(6):1049-1068. https://doi.org/10.3852/16-130