Publication: Single-Strand Conformation Polymorphism Fingerprint Method for Dictyostelids
Issued Date
2021-08-27
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ISSN
1664302X
Other identifier(s)
2-s2.0-85114865845
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Mahidol University
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SCOPUS
Bibliographic Citation
Frontiers in Microbiology. Vol.12, (2021)
Suggested Citation
Phongthana Pasookhush, Asmatullah Usmani, Kowit Suwannahong, Prasit Palittapongarnpim, Kamolchanok Rukseree, Kanchiyaphat Ariyachaokun, Sureemas Buates, Suradej Siripattanapipong, Pravech Ajawatanawong Single-Strand Conformation Polymorphism Fingerprint Method for Dictyostelids. Frontiers in Microbiology. Vol.12, (2021). doi:10.3389/fmicb.2021.708685 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/77241
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Title
Single-Strand Conformation Polymorphism Fingerprint Method for Dictyostelids
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.