Distinction of Paramecium strains by a combination method of RAPD analysis and multiplex PCR

Sonoko Matsumoto; Kenta Watanabe; Hiroko Kiyota; Masato Tachibana; Takashi Shimizu; Masahisa Watarai

doi:10.1371/journal.pone.0265139

Distinction of Paramecium strains by a combination method of RAPD analysis and multiplex PCR

PLoS One. 2022 Mar 11;17(3):e0265139. doi: 10.1371/journal.pone.0265139. eCollection 2022.

Authors

Sonoko Matsumoto¹, Kenta Watanabe^{1

2}, Hiroko Kiyota², Masato Tachibana³, Takashi Shimizu^{1

2}, Masahisa Watarai^{1

2}

Affiliations

¹ Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan.
² Joint Faculty of Veterinary Medicine, Laboratory of Veterinary Public Health, Yamaguchi University, Yamaguchi, Japan.
³ Joint Faculty of Veterinary Medicine, National BioResource Project Paramecium, Yamaguchi University, Yamaguchi, Japan.

Abstract

Paramecium is employed as a valuable model organism in various research fields since a large number of strains with different characteristics of size, morphology, degree of aging, and type of conjugation can be obtained. It is necessary to determine a method for the classification and simple identification of strains to increase their utility as a research tool. This study attempted to establish a polymerase chain reaction (PCR)-based method to differentiate strains of the same species. Genomic DNA was purified from several strains of P. caudatum, P. tetraurelia, and P. bursaria used for comparison by the random amplified polymorphic DNA (RAPD)-PCR method. In P. tetraurelia and P. bursaria, it was sufficiently possible to distinguish specific strains depending on the pattern of random primers and amplification characteristics. For the classification of P. caudatum, based on the sequence data obtained by RAPD-PCR analysis, 5 specific primer sets were designed and a multiplex PCR method was developed. The comparative analysis of 2 standard strains, 12 recommended strains, and 12 other strains of P. caudatum provided by the National BioResource Project was conducted, and specific strains were identified. This multiplex PCR method would be an effective tool for the simple identification of environmental isolates or the management of Paramecium strains.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Multiplex Polymerase Chain Reaction
Paramecium* / genetics
Random Amplified Polymorphic DNA Technique / methods

Grants and funding

This study was supported in part by the Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research (C) and (B) under grant nos. 19K06383 and 17H03914 to K.W. and M.W. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.