Please use this identifier to cite or link to this item: https://ir.swu.ac.th/jspui/handle/123456789/14101
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dc.contributor.authorSuwannasai N.
dc.contributor.authorMartín M.P.
dc.contributor.authorPhosri C.
dc.contributor.authorSihanonth P.
dc.contributor.authorWhalley A.J.S.
dc.contributor.authorSpouge J.L.
dc.date.accessioned2021-04-05T03:33:11Z-
dc.date.available2021-04-05T03:33:11Z-
dc.date.issued2013
dc.identifier.issn19326203
dc.identifier.other2-s2.0-84873500605
dc.identifier.urihttps://ir.swu.ac.th/jspui/handle/123456789/14101-
dc.identifier.urihttps://www.scopus.com/inward/record.uri?eid=2-s2.0-84873500605&doi=10.1371%2fjournal.pone.0054529&partnerID=40&md5=2a0df158f3df4d7ba85e69f6840227fa
dc.description.abstractThailand, a part of the Indo-Burma biodiversity hotspot, has many endemic animals and plants. Some of its fungal species are difficult to recognize and separate, complicating assessments of biodiversity. We assessed species diversity within the fungal genera Annulohypoxylon and Hypoxylon, which produce biologically active and potentially therapeutic compounds, by applying classical taxonomic methods to 552 teleomorphs collected from across Thailand. Using probability of correct identification (PCI), we also assessed the efficacy of automated species identification with a fungal barcode marker, ITS, in the model system of Annulohypoxylon and Hypoxylon. The 552 teleomorphs yielded 137 ITS sequences; in addition, we examined 128 GenBank ITS sequences, to assess biases in evaluating a DNA barcode with GenBank data. The use of multiple sequence alignment in a barcode database like BOLD raises some concerns about non-protein barcode markers like ITS, so we also compared species identification using different alignment methods. Our results suggest the following. (1) Multiple sequence alignment of ITS sequences is competitive with pairwise alignment when identifying species, so BOLD should be able to preserve its present bioinformatics workflow for species identification for ITS, and possibly therefore with at least some other non-protein barcode markers. (2) Automated species identification is insensitive to a specific choice of evolutionary distance, contributing to resolution of a current debate in DNA barcoding. (3) Statistical methods are available to address, at least partially, the possibility of expert misidentification of species. Phylogenetic trees discovered a cryptic species and strongly supported monophyletic clades for many Annulohypoxylon and Hypoxylon species, suggesting that ITS can contribute usefully to a barcode for these fungi. The PCIs here, derived solely from ITS, suggest that a fungal barcode will require secondary markers in Annulohypoxylon and Hypoxylon, however. The URL http://tinyurl.com/spouge-barcode contains computer programs and other supplementary material relevant to this article.
dc.subjectinternal transcribed spacer
dc.subjectAnnulohypoxylon
dc.subjectarticle
dc.subjectBOLD signal
dc.subjectcladistics
dc.subjectcomputer program
dc.subjectcontrolled study
dc.subjectDNA barcoding
dc.subjectfungus
dc.subjectfungus identification
dc.subjectgene sequence
dc.subjectgenetic database
dc.subjectgenetic distance
dc.subjectHypoxylon
dc.subjectmonophyly
dc.subjectnonhuman
dc.subjectphylogenetic tree
dc.subjectsequence alignment
dc.subjectspecies diversity
dc.subjectspecies identification
dc.subjecttaxonomic rank
dc.subjectteleomorph
dc.subjectThailand
dc.subjectBase Sequence
dc.subjectBiodiversity
dc.subjectComputational Biology
dc.subjectDNA Barcoding, Taxonomic
dc.subjectDNA, Intergenic
dc.subjectInternet
dc.subjectMolecular Sequence Data
dc.subjectPhylogeny
dc.subjectSequence Alignment
dc.subjectSequence Analysis, DNA
dc.subjectSpecies Specificity
dc.subjectThailand
dc.subjectXylariales
dc.titleFungi in Thailand: A Case Study of the Efficacy of an ITS Barcode for Automatically Identifying Species within the Annulohypoxylon and Hypoxylon Genera
dc.typeArticle
dc.rights.holderScopus
dc.identifier.bibliograpycitationPLoS ONE. Vol 8, No.2 (2013), p.-
dc.identifier.doi10.1371/journal.pone.0054529
Appears in Collections:Scopus 1983-2021

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