Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon

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Abstract

The large number of species still to be discovered in fungi, together with an exponentially growing number of environmental sequences that cannot be linked to known taxa, has fuelled the idea that it might be necessary to formally name fungi on the basis of sequence data only. Here we object to this idea due to several shortcomings of the approach, ranging from concerns regarding reproducibility and the violation of general scientific principles to ethical issues. We come to the conclusion that sequence-based nomenclature is potentially harmful for mycology as a discipline. Additionally, a classification based on sequences as types is not within reach anytime soon, because there is a lack of consensus regarding common standards due to the fast pace at which sequencing technologies develop.

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Most cited references 69

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Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous.

K. O'Donnell, E Cigelnik (1997)

The evolutionary history of the phytopathogenic Gibberella fujikuroi complex of Fusarium and related species was investigated by cladistic analysis of DNA sequences obtained from multiple unlinked loci. Gene phylogenies inferred from the mitochondrial small subunit (mtSSU) rDNA, nuclear 28S rDNA, and beta-tubulin gene were generally concordant, providing strong support for a fully resolved phylogeny of all biological and most morphological species. Discordance of the nuclear rDNA internal transcribed spacer 2 (ITS2) gene tree is due to paralogous or xenologous ITS2 sequences. PCR and sequence analysis demonstrated that every strain of the ingroup species tested possesses two highly divergent nonorthologous ITS2 types designated type I and type II. Only the major ITS2 type, however, is discernable when PCR products are amplified and sequenced directly with conserved primers. The minor ITS2 type was recovered using ITS2 type-specific PCR primers. Distribution of the major ITS2 type within the species lineages exhibits a homoplastic pattern of evolution, thus obscuring true phylogenetic relationships. The results suggest that the ancestral ITS2 types may have arisen following an ancient interspecific hybridization or gene duplication which occurred prior to the evolutionary radiation of the Gibberella fujikuroi complex and related species of Fusarium. The results also indicate that current morphological-based taxonomic schemes for these fungi are unnatural and a new classification is required.

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Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex.

Micah Hamady, Jeffrey Walker, J Kirk Harris … (2008)

We constructed error-correcting DNA barcodes that allow one run of a massively parallel pyrosequencer to process up to 1,544 samples simultaneously. Using these barcodes we processed bacterial 16S rRNA gene sequences representing microbial communities in 286 environmental samples, corrected 92% of sample assignment errors, and thus characterized nearly as many 16S rRNA genes as have been sequenced to date by Sanger sequencing.

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Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding.

Alice Valentini, Pierre Taberlet, Claude Miaud … (2016)

Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90-0.99) vs. 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.

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Author and article information

Journal

Journal ID (nlm-ta): IMA Fungus

Journal ID (iso-abbrev): IMA Fungus

Journal ID (publisher-id): IMA Fungus

Title: IMA Fungus

Publisher: International Mycological Association

ISSN (Print): 2210-6340

ISSN (Electronic): 2210-6359

Publication date (Electronic): 28 May 2018

Publication date (Print): June 2018

Volume: 9

Issue: 1

Pages: 177-183

Affiliations

[1 ]Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60483 Frankfurt am Main, Germany;

[2 ]Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany

[3 ]Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands

[4 ]Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA

[5 ]Genetic Resources Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan

[6 ]State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China

[7 ]Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand

[8 ]Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA

[9 ]Department of Plant Biology, Rutgers University, 59 Dudley Road, Foran Hall 201, New Brunswick, New Jersey 08901, USA

[10 ]Department of Microbial Drugs, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, D-38124 Braunschweig, Germany

Author notes

corresponding author e-mail: m.thines@ 123456thines-lab.eu

Article

DOI: 10.5598/imafungus.2018.09.01.11

PMC ID: 6048572

PubMed ID: 30018878

SO-VID: 7965b113-a557-49df-8be4-665ccc37dc25

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Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon

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Abstract

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Taxonomic intelligence

Most cited references 69

Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous.

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex.

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding.

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