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Using high-throughput amplicon sequencing to evaluate intragenomic variation and accuracy in species identification of cordyceps species
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Document Title
Using high-throughput amplicon sequencing to evaluate intragenomic variation and accuracy in species identification of cordyceps species
Author
Paloi S., Mhuantong W., Luangsa-Ard J.J., Kobmoo N.
Name from Authors Collection
Affiliations
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Development Agency (NSTDA), 113 Thailand Science Park, Phahonuyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
Type
Article
Source Title
Journal of Fungi
ISSN
2309608X
Year
2021
Volume
7
Issue
9
Open Access
All Open Access, Gold, Green
Publisher
MDPI
DOI
10.3390/jof7090767
Format
Abstract
While recent sequencing technologies (third generation sequencing) can successfully sequence all copies of nuclear ribosomal DNA (rDNA) markers present within a genome and offer insights into the intragenomic variation of these markers, high intragenomic variation can be a source of confusion for high-throughput species identification using such technologies. High-throughput (HT) amplicon sequencing via PacBio SEQUEL I was used to evaluate the intragenomic variation of the ITS region and D1–D2 LSU domains in nine Cordyceps species, and the accuracy of such technology to identify these species based on molecular phylogenies was also assessed. PacBio sequences within strains showed variable level of intragenomic variation among the studied Cordyceps species with C. blackwelliae showing greater variation than the others. Some variants from a mix of species clustered together outside their respective species of origin, indicative of intragenomic variation that escaped concerted evolution shared between species. Proper selection of consensus sequences from HT amplicon sequencing is a challenge for interpretation of correct species identification. PacBio consensus sequences with the highest number of reads represent the major variants within a genome and gave the best results in terms of species identification. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.
Keyword
Barcoding | Cordyceps | Intragenomic variation | NrDNA | PacBio sequencing
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
Funding Sponsor
National Center for Genetic Engineering and Biotechnology
Funding Number
P1950231
License
CC BY
Rights
N/A
Publication Source
Scopus