dc.contributor.author
Lücking, Robert
dc.contributor.author
Truong, Ba Vuong
dc.contributor.author
Huong, Dang Thi Thu
dc.contributor.author
Le, Ngoc Han
dc.contributor.author
Nguyen, Quoc Dat
dc.contributor.author
Nguyen, Van Dat
dc.contributor.author
Raab-Straube, Eckhard von
dc.contributor.author
Bollendorff, Sarah
dc.contributor.author
Govers, Kim
dc.contributor.author
Di Vincenzo, Vanessa
dc.date.accessioned
2021-02-10T10:59:21Z
dc.date.available
2021-02-10T10:59:21Z
dc.identifier.uri
https://refubium.fu-berlin.de/handle/fub188/29577
dc.identifier.uri
http://dx.doi.org/10.17169/refubium-29321
dc.description.abstract
DNA barcoding using the nuclear internal transcribed spacer (ITS) has become prevalent in surveys of fungal diversity. This approach is, however, associated with numerous caveats, including the desire for speed, rather than accuracy, through the use of automated analytical pipelines, and the shortcomings of reference sequence repositories. Here we use the case of a specimen of the bracket fungus Trametes s.lat. (which includes the common and widespread turkey tail, T. versicolor) to illustrate these problems. The material was collected in Vietnam as part of a biodiversity inventory including DNA barcoding approaches for arthropods, plants and fungi. The ITS barcoding sequence of the query taxon was compared against reference sequences in GenBank and the curated fungal ITS database UNITE, using BLASTn and MegaBLAST, and was subsequently analysed in a multiple alignment-based phylogenetic context through a maximum likelihood tree including related sequences. Our results initially indicated issues with BLAST searches, including the use of Frairwise local alignments and sorting through Total score and E value, rather than Percentage identity, as major shortcomings of the DNA barcoding approach. However, after thorough analysis of the results, we concluded that the single most important problem of this approach was incorrect sequence labelling, calling for the implementation of third-party annotations or analogous approaches in primary sequence repositories. In addition, this particular example revealed problems of improper fungal nomenclature, which required reinstatement of the genus name Cubamyces (= Leioirametes), with three new combinations: C. flavidus, C lactineus and C. menziesii. The latter was revealed as the correct identification of the query taxon, although the name did not appear among the best BLAST hits. While the best BLAST hits did correspond to the target taxon in terms of sequence data, their label names were misleading or unresolved, including [Fungal endophyte], [Uncultured fungus], Basidiomycota, Trametes cf. cubensis, Lenzites elegans and Geotrichum candidum (an unrelated ascomycetous contaminant). Our study demonstrates that accurate identification of fungi through molecular barcoding is currently not a fast-track approach that can be achieved through automated pipelines.
en
dc.format.extent
22 Seiten
dc.rights.uri
https://creativecommons.org/licenses/by/4.0/
dc.subject
Basidiomycota
en
dc.subject
fungal barcoding
en
dc.subject
sequence contamination
en
dc.subject
Trametes cubensis
en
dc.subject
Trametes menziesii
en
dc.subject.ddc
500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::579 Mikroorganismen, Pilze, Algen
dc.title
Caveats of fungal barcoding: a case study in Trametes s.lat. (Basidiomycota: Polyporales) in Vietnam reveals multiple issues with mislabelled reference sequences and calls for third-party annotations
dc.type
Wissenschaftlicher Artikel
dcterms.bibliographicCitation.doi
10.3372/wi.50.50302
dcterms.bibliographicCitation.journaltitle
Willdenowia
dcterms.bibliographicCitation.number
3
dcterms.bibliographicCitation.pagestart
383
dcterms.bibliographicCitation.pageend
403
dcterms.bibliographicCitation.volume
50
dcterms.bibliographicCitation.url
https://doi.org/10.3372/wi.50.50302
refubium.affiliation
Botanischer Garten und Botanisches Museum Berlin-Dahlem (BGBM)
refubium.resourceType.isindependentpub
no
dcterms.accessRights.openaire
open access
dcterms.isPartOf.issn
0511-9618
dcterms.isPartOf.eissn
1868-6397
refubium.resourceType.provider
WoS-Alert