Determining threshold values for barcoding fungi: lessons from<i>Cortinarius</i>(Basidiomycota), a highly diverse and widespread ectomycorrhizal genus

Garnica, Sigisfredo; Schön, Max Emil; Abarenkov, Kessy; Riess, Kai; Liimatainen, Kare; Niskanen, Tuula; Dima, Bálint; Soop, Karl; Frøslev, Tobias Guldberg; Jeppesen, Thomas Stjernegaard; Peintner, Ursula; Kuhnert‐Finkernagel, Regina; Brandrud, Tor Erik; Saar, Günter; Oertel, B.; Ammirati, Joseph F.

doi:10.1093/femsec/fiw045

Cited by 101 publications

(121 citation statements)

References 82 publications

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“…Gray is less variable than RPB2 but it performs as well as RPB2 and RPB1 to retrieve supported close relationships in the phylogeny (Frøslev et al 2005). However, out of 901 species, 30-39 species (depending on alignment method) could not be separated based on full ITS sequences owing to a lack of a barcoding gap (Garnica et al 2016). ''In a very few cases, there is evidence of 'morphological species': a morphologically and ecogeographically distinguishable species/subspecies with identical ITS regions, e.g.…”

Section: Case Studies From Basidiomycotamentioning

confidence: 98%

“…The use of mgDNA in naming fungal taxa in these pathogenic genera would cause serious problems, as it is based on overall sequence identity between the query sequence as well as those in the reference databases. At present, 97% or greater sequence identity for OTU/species is used for species delimitation, identification and assessment of species numbers (O'Brien et al 2005;Nilsson et al 2008;Tedersoo et al 2014;Garnica et al 2016;Dissanayake et al 2018;Jayawardena et al 2018b). However, there is a large range of intra-and interspecific ITS sequence variation depending on the taxonomic groups .…”

Section: The Cryptic Speciesmentioning

confidence: 99%

“…ionochlorus Maire (Brandrud et al 1990(Brandrud et al , 1992(Brandrud et al , 1994(Brandrud et al , 1998(Brandrud et al , 2012Garnica et al 2016). More importantly, up to 40% false positives (wrongly splitting species) were obtained with full ITS regions sequences in subgenus Myxacium (Garnica et al 2016). Harder et al (2013) used a two single-copy nuclear genes dataset to study Mycena pura (Pers.)…”

Section: Case Studies From Basidiomycotamentioning

confidence: 99%

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Can we use environmental DNA as holotypes?

et al. 2018

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The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community. The idea of using intracellular DNA (''mgDNA'') from environmental samples as holotypes seems at face value, to be a good idea, considering the expansion of knowledge among these 'dark taxa' or 'dark matter fungi' that it could provide (i.e. sequence based taxa without physical specimens and formal nomenclature). However, the limitations of using mgDNA as holotypes needs careful thought, i.e. can we use a short mgDNA fragment, which may contain a small amount of genetic information, to allow discrimination between species? What is the point and are the potential problems of giving valid scientific names to mgDNA? Numerous mycologists and taxonomists, who have many years of experience working on the taxonomy and phylogeny of different groups of fungi, are concerned about the consequences of providing valid names to mgDNA. There has been much debate, through several publications on the considerable problems of using mgDNA as holotypes. The proponents have tried to debate the virtues of using mgDNA as holotypes. Those against have shown that identification to species using mgDNA does not work in many fungal groups, while those for have shown cases where species can be identified with mgDNA. Different disciplines have different reasons and opinions for using mgDNA as holotypes, however even groups of the same disciplines have dissimilar ideas. In this paper we explore the use of mgDNA as holotypes. We provide evidences and opinions as to the use of mgDNA as holotypes from our own experiences. In no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa, but relate the issues to fungal taxonomy. In fact we show the value of using sequence data from these approaches, in dealing with the discovery of already named taxa, taxa numbers and ecological roles. We discuss the advantages and the pitfalls of using mgDNA from environmental samples as holotypes. The impacts of expanding the nomenclatural concept to allow using mgDNA from environmental samples as holotypes are also discussed. We provide evidence from case studies on Botryosphaeria, Colletotrichum, Penicillium and Xylaria. The case studies show that we cannot use mgDNA due to their short fragments and the fact that most ITS sequence data presently result from environmental sequencing. We conclude from the evidence that it is highly undesirable to use mgDNA as holotypes in naming fungal species. If this approach adopted, it would result in numerous problems where species identification cannot be confirmed due to limited sequence data available for the holotypes. We also propose an alternative DNA-based system for naming DNA based species which would provide considerably less problems and should be adopted.

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Section: Case Studies From Basidiomycotamentioning

confidence: 98%

Section: The Cryptic Speciesmentioning

confidence: 99%

Section: Case Studies From Basidiomycotamentioning

confidence: 99%

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Can we use environmental DNA as holotypes?

et al. 2018

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“…Therefore, we suggest from the chemotaxonomical point of view through the occurrence of the mono-Omethylated pigments such as 7,7'-emodinphyscion (1) and flavomannin C (5) in D. nahuelbutensis, that Chilean Dermocybe species present a separate linage in evolution of Dermocybe, which is more related to species of the Northern hemisphere than to Australasian species. This suggestion, based on pigmentchemical characters is meanwhile also supported on DNA level by the use of DNA sequences for recent phylogenetic studies in genus Cortinarius including Dermocybe [29].…”

Section: 7'-emodinphyscionmentioning

confidence: 74%

Pigment pattern of the Chilean mushroom Dermocybe nahuelbutensis Garrido & E. Horak

Greff¹,

Porzel²,

Schmidt³

et al. 2017

Rec.Nat.Prod.

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Fruiting bodies of the Chilean mushroom Dermocybe nahuelbutenis Garrido & E. Horak (syn.: Cortinarius nahuelbutensis (Garrido & E. Horak) E. Valenz. & G. Moreno) were chemically investigated for the first time and afforded the new dimeric anthraqinone 7,7'-emodinphyscion (1) beside the know anthraquinones dermolutein (2), endocrocin (3), skyrin (4) and the dimeric pre-anthraquinone derivative flavomannin C (5). The chemotaxonomic significance of the pigments is discussed.

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“…Our approach relied on genome-derived ITS sequences, and we quantified deviations from the genome sequences among conspecific ITS sequences in the INSDC as assessed through species names (Latin binomials). However, some degree of deviation from the genome-derived sequences is expected, since intraspecific ITS variation may reach 3% or in some cases more (Schoch et al 2012, Garnica et al 2016. Similarly, the multicopy nature of the ITS region is a potential complication in that we may inadvertently have used a rare and perhaps deviant genome ITS copy and compared it to more common ITS copies (cf.…”

Section: Discussionmentioning

confidence: 99%

Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory

Nilsson¹,

Sánchez-García²,

Ryberg³

et al. 2017

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DNA sequences are increasingly used for taxonomic and functional assessment of environmental communities. In mycology, the nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen marker for such pursuits. Molecular identification is associated with many challenges, one of which is low read quality of the reference sequences used for inference of taxonomic and functional properties of the newly sequenced community (or single taxon). This study investigates whether public fungal ITS sequences are subjected to sufficient trimming in their distal (5' and 3') ends prior to deposition in the public repositories. We examined 86 species (and 10,584 sequences) across the fungal tree of life, and we found that on average 13.1% of the sequences were poorly trimmed in one or both of their 5' and 3' ends. Deposition of poorly trimmed entries was found to continue through 2016. Poorly trimmed reference sequences add noise and mask biological signal in sequence similarity searches and phylogenetic analyses, and we provide a set of recommendations on how to manage the sequence trimming problem.

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Determining threshold values for barcoding fungi: lessons fromCortinarius(Basidiomycota), a highly diverse and widespread ectomycorrhizal genus

Cited by 101 publications

References 82 publications

Can we use environmental DNA as holotypes?

Can we use environmental DNA as holotypes?

Pigment pattern of the Chilean mushroom Dermocybe nahuelbutensis Garrido & E. Horak

Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory

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