Please use this identifier to cite or link to this item: https://ir.swu.ac.th/jspui/handle/123456789/14101
ชื่อเรื่อง: Fungi in Thailand: A Case Study of the Efficacy of an ITS Barcode for Automatically Identifying Species within the Annulohypoxylon and Hypoxylon Genera
ผู้แต่ง: Suwannasai N.
Martín M.P.
Phosri C.
Sihanonth P.
Whalley A.J.S.
Spouge J.L.
Keywords: internal transcribed spacer
Annulohypoxylon
article
BOLD signal
cladistics
computer program
controlled study
DNA barcoding
fungus
fungus identification
gene sequence
genetic database
genetic distance
Hypoxylon
monophyly
nonhuman
phylogenetic tree
sequence alignment
species diversity
species identification
taxonomic rank
teleomorph
Thailand
Base Sequence
Biodiversity
Computational Biology
DNA Barcoding, Taxonomic
DNA, Intergenic
Internet
Molecular Sequence Data
Phylogeny
Sequence Alignment
Sequence Analysis, DNA
Species Specificity
Thailand
Xylariales
วันที่เผยแพร่: 2013
บทคัดย่อ: Thailand, 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.
URI: https://ir.swu.ac.th/jspui/handle/123456789/14101
https://www.scopus.com/inward/record.uri?eid=2-s2.0-84873500605&doi=10.1371%2fjournal.pone.0054529&partnerID=40&md5=2a0df158f3df4d7ba85e69f6840227fa
ISSN: 19326203
Appears in Collections:Scopus 1983-2021

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