2016
DOI: 10.1093/femsec/fiw045
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Determining threshold values for barcoding fungi: lessons fromCortinarius(Basidiomycota), a highly diverse and widespread ectomycorrhizal genus

Abstract: Different distance-based threshold selection approaches were used to assess and compare use of the internal transcribed spacer (ITS) region to distinguish among 901 Cortinarius species represented by >3000 collections. Sources of error associated with genetic markers and selection approaches were explored and evaluated using MOTUs from genus and lineage based-alignments. Our study indicates that 1%-2% more species can be distinguished by using the full-length ITS barcode as compared to either the ITS1 or ITS2 … Show more

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Cited by 101 publications
(121 citation statements)
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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%
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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%
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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%
“…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%