Comparative genome analysis of test algal strain NIVA-CHL1 (Raphidocelis subcapitata) maintained in microalgal culture collections worldwide

• Published in: PloS one Vol. 15; no. 11; p. e0241889
• Main Authors: Yamagishi, Takahiro, Yamaguchi, Haruyo, Suzuki, Shigekatsu, Yoshikawa, Mayumi, Jameson, Ian, Lorenz, Maike, Nobles, David R, Campbell, Christine, Seki, Masanori, Kawachi, Masanobu, Yamamoto, Hiroshi
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 09.11.2020; Public Library of Science (PLoS)
• Subjects: Algae; Algal growth; Algal Proteins - drug effects; Algal Proteins - genetics; Aquatic microorganisms; Biology; Biology and Life Sciences; Chlorine compounds; Chlorophyceae - drug effects; Chlorophyceae - genetics; Chlorophyceae - growth & development; Collaboration; Comparative analysis; Computer and Information Sciences; Conductance; Culture; Culture collections; Culture Media - chemistry; Ecosystem biology; Environmental studies; Gene Expression Regulation - drug effects; Gene mutation; Gene sequencing; Genetic aspects; Genomes; Growth inhibition test; Industrial research; Ion channels; Japan; Laboratories; Mutation; Nucleotide sequence; Nucleotides; Phylogenetics; Physical Sciences; Physiology; Polymorphism, Single Nucleotide; Proteins; Raphidocelis subcapitata; Resistance; Risk assessment; Single-nucleotide polymorphism; Sodium chloride; Sodium Chloride - pharmacology; Varieties; Whole Genome Sequencing - methods; Japan; England; United Kingdom > UK; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0241889

Raphidocelis subcapitata is one of the most frequently used species for algal growth inhibition tests. Accordingly, many microalgal culture collections worldwide maintain R. subcapitata for distribution to users. All R. subcapitata strains maintained in these collections are derived from the same cultured strain, NIVA-CHL1. However, considering that 61 years have passed since this strain was isolated, we suspected that NIVA-CHL1 in culture collections might have acquired various mutations. In this study, we compared the genome sequences among NIVA-CHL1 from 8 microalgal culture collections and one laboratory in Japan to evaluate the presence of mutations. We found single-nucleotide polymorphisms or indels at 19,576 to 28,212 sites per strain in comparison with the genome sequence of R. subcapitata NIES-35, maintained at the National Institute for Environmental Studies, Tsukuba, Japan. These mutations were detected not only in non-coding but also in coding regions; some of the latter mutations may affect protein function. In growth inhibition test with 3,5-dichlorophenol, EC50 values varied 2.6-fold among the 9 strains. In the ATCC 22662-2 and CCAP 278/4 strains, we also detected a mutation in the gene encoding small-conductance mechanosensitive ion channel, which may lead to protein truncation and loss of function. Growth inhibition test with sodium chloride suggested that osmotic regulation has changed in ATCC 22662-2 and CCAP 278/4 in comparison with NIES-35.