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Single-Strand Conformation Polymorphism Fingerprint Method for Dictyostelids
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Document Title
Single-Strand Conformation Polymorphism Fingerprint Method for Dictyostelids
Author
Pasookhush P.,Usmani A.,Suwannahong K.,Palittapongarnpim P.,Rukseree K.,Ariyachaokun K.,Buates S.,Siripattanapipong S.,Ajawatanawong P.
Name from Authors Collection
Affiliations
Division of Bioinformatics and Data Management for Research, Research Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand; Department of Biology, Faculty of Education, Kandahar University, Kandahar, Afghanistan; Department of Environmental Health, Faculty of Public Health, Burapa University, Chonburi, Thailand; National Science and Technology Development Agency (NSTDA), Thailand Science Park, Khlong Nueng, Thailand; Department of Sciences and Liberal Arts, Mahidol University, Amnatcharoen Campus, Bung, Thailand; Department of Biological Sciences, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, Thailand
Type
Article
Source Title
Frontiers in Microbiology
ISSN
1664302X
Year
2021
Volume
12
Open Access
All Open Access, Gold, Green
Publisher
Frontiers Media S.A.
DOI
10.3389/fmicb.2021.708685
Abstract
Dictyostelid social amoebae are a highly diverse group of eukaryotic soil microbes that are valuable resources for biological research. Genetic diversity study of these organisms solely relies on molecular phylogenetics of the SSU rDNA gene, which is not ideal for large-scale genetic diversity study. Here, we designed a set of PCR–single-strand conformation polymorphism (SSCP) primers and optimized the SSCP fingerprint method for the screening of dictyostelids. The optimized SSCP condition required gel purification of the SSCP amplicons followed by electrophoresis using a 9% polyacrylamide gel under 4°C. We also tested the optimized SSCP procedure with 73 Thai isolates of dictyostelid that had the SSU rDNA gene sequences published. The SSCP fingerprint patterns were related to the genus-level taxonomy of dictyostelids, but the fingerprint dendrogram did not reflect the deep phylogeny. This method is rapid, cost-effective, and suitable for large-scale sample screening as compared with the phylogenetic analysis of the SSU rDNA gene sequences. © Copyright © 2021 Pasookhush, Usmani, Suwannahong, Palittapongarnpim, Rukseree, Ariyachaokun, Buates, Siripattanapipong and Ajawatanawong.
Keyword
Dictyostelids | Diversity | fingerprint | SSCP | SSU rDNA gene
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
Funding Sponsor
Ministry of Higher Education, Malaysia; Mahidol University; Thailand Science Research and Innovation
License
CC BY
Rights
Author
Publication Source
Scopus