Formal description of sequence-based voucherless Fungi : promises and pitfalls, and how to resolve them

IMA Fungus
Robert Lücking, David L Hawksworth

Abstract

There is urgent need for a formal nomenclature of sequence-based, voucherless Fungi, given that environmental sequencing has accumulated more than one billion fungal ITS reads in the Sequence Read Archive, about 1,000 times as many as fungal ITS sequences in GenBank. These unnamed Fungi could help to bridge the gap between 115,000 to 140,000 currently accepted and 2.2 to 3.8 million predicted species, a gap that cannot realistically be filled using specimen or culture-based inventories. The Code never aimed at placing restrictions on the nature of characters chosen for taxonomy, and the requirement for physical types is now becoming a constraint on the advancement of science. We elaborate on the promises and pitfalls of sequence-based nomenclature and provide potential solutions to major concerns of the mycological community. Types of sequence-based taxa, which by default lack a physical specimen or culture, could be designated in four alternative ways: (1) the underlying sample ('bag' type), (2) the DNA extract, (3) fluorescent in situ hybridization (FISH), or (4) the type sequence itself. Only (4) would require changes to the Code and the latter would be the most straightforward approach, complying with three of the five prin...Continue Reading

References

Nov 1, 1996·Molecular Biology and Evolution·M A Hershkovitz, L A Lewis
Jan 23, 1999·American Journal of Human Genetics·D Liao
Jul 6, 2000·Comptes rendus de l'Académie des sciences. Série III, Sciences de la vie·A HassaninS Tillier
Dec 16, 2000·Fungal Genetics and Biology : FG & B·J W TaylorM C Fisher
Jun 19, 2002·Molecular Phylogenetics and Evolution·Kwan Soo Ko, Hack Sung Jung
Jul 9, 2002·Molecular Phylogenetics and Evolution·Jean-Marc MoncalvoOrson K Miller
Nov 30, 2002·Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences·Mostafa Ronaghi, Elahe Elahi
Sep 19, 2003·Molecular Phylogenetics and Evolution·Leslie R GoertzenRobert K Jansen
Oct 16, 2003·Biological Reviews of the Cambridge Philosophical Society·Brian K Hall
Dec 13, 2003·Proceedings of the National Academy of Sciences of the United States of America·A Elizabeth ArnoldEdward Allen Herre
Apr 10, 2004·Bioinformatics·Thomas HuberPhilip Hugenholtz
Sep 17, 2004·Systematic Biology·John Wiens
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Sep 10, 2005·Applied and Environmental Microbiology·Heath E O'BrienRytas Vilgalys
Oct 26, 2005·Systematic Biology·Kipling W WillQuentin D Wheeler
Nov 3, 2005·Evolution; International Journal of Organic Evolution·A PringleJ W Taylor
Dec 8, 2005·Applied and Environmental Microbiology·Kevin E AshelfordAndrew J Weightman
May 9, 2006·Bioinformatics·Marc A Suchard, Benjamin D Redelings
Aug 2, 2006·Proceedings of the National Academy of Sciences of the United States of America·Mitchell L SoginGerhard J Herndl
Oct 13, 2006·Annual Review of Psychology·Michael I Posner, Mary K Rothbart
Oct 20, 2006·Nature·Timothy Y JamesRytas Vilgalys
Jun 19, 2007·Mycological Research·David S HibbettNing Zhang
Jul 31, 2007·Genome Biology·Susan M HuseDavid Mark Welch
Jan 24, 2008·The New Phytologist·Thomas D BrunsKaren W Hughes
Mar 22, 2008·Science·M I Bidartondo
Aug 13, 2008·Proceedings of the National Academy of Sciences of the United States of America·David B Wake, Vance T Vredenburg
Aug 30, 2008·Molecular Biology and Evolution·Uwe K Simon, Michael Weiss
Oct 7, 2008·Mycologia·József GemlD Lee Taylor

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Citations

Apr 17, 2019·Journal of Medical Microbiology·G RebouxL Millon
Jul 15, 2020·Annual Review of Microbiology·Timothy Y JamesAntonis Rokas
Nov 18, 2018·Nature Reviews. Microbiology·R Henrik NilssonLeho Tedersoo
Oct 24, 2018·Nature Ecology & Evolution
Dec 29, 2020·Medical Mycology·Leyna DíazF Javier Cabañes
Oct 30, 2020·Journal of Fungi·Cene Gostinčar
Apr 28, 2021·Nature Microbiology·Robert LückingConrad L Schoch
Jun 20, 2021·Mycoses·Danuta Nowicka, Urszula Nawrot

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Methods Mentioned

BETA
PCR
amplicon sequencing

Software Mentioned

Phy
Guidance
BAS
MAFFT
Ord
PICS
RAxML
UNITE
SATe
USEARCH

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