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Comparative genome analysis of test algal strain NIVA-CHL1 (Raphidocelis subcapitata) maintained in microalgal culture collections worldwide
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 cu...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7652255/ https://www.ncbi.nlm.nih.gov/pubmed/33166324 http://dx.doi.org/10.1371/journal.pone.0241889 |
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author | Yamagishi, Takahiro Yamaguchi, Haruyo Suzuki, Shigekatsu Yoshikawa, Mayumi Jameson, Ian Lorenz, Maike Nobles, David R. Campbell, Christine Seki, Masanori Kawachi, Masanobu Yamamoto, Hiroshi |
author_facet | Yamagishi, Takahiro Yamaguchi, Haruyo Suzuki, Shigekatsu Yoshikawa, Mayumi Jameson, Ian Lorenz, Maike Nobles, David R. Campbell, Christine Seki, Masanori Kawachi, Masanobu Yamamoto, Hiroshi |
author_sort | Yamagishi, Takahiro |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7652255 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-76522552020-11-18 Comparative genome analysis of test algal strain NIVA-CHL1 (Raphidocelis subcapitata) maintained in microalgal culture collections worldwide Yamagishi, Takahiro Yamaguchi, Haruyo Suzuki, Shigekatsu Yoshikawa, Mayumi Jameson, Ian Lorenz, Maike Nobles, David R. Campbell, Christine Seki, Masanori Kawachi, Masanobu Yamamoto, Hiroshi PLoS One Research Article 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. Public Library of Science 2020-11-09 /pmc/articles/PMC7652255/ /pubmed/33166324 http://dx.doi.org/10.1371/journal.pone.0241889 Text en © 2020 Yamagishi et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Yamagishi, Takahiro Yamaguchi, Haruyo Suzuki, Shigekatsu Yoshikawa, Mayumi Jameson, Ian Lorenz, Maike Nobles, David R. Campbell, Christine Seki, Masanori Kawachi, Masanobu Yamamoto, Hiroshi Comparative genome analysis of test algal strain NIVA-CHL1 (Raphidocelis subcapitata) maintained in microalgal culture collections worldwide |
title | Comparative genome analysis of test algal strain NIVA-CHL1 (Raphidocelis subcapitata) maintained in microalgal culture collections worldwide |
title_full | Comparative genome analysis of test algal strain NIVA-CHL1 (Raphidocelis subcapitata) maintained in microalgal culture collections worldwide |
title_fullStr | Comparative genome analysis of test algal strain NIVA-CHL1 (Raphidocelis subcapitata) maintained in microalgal culture collections worldwide |
title_full_unstemmed | Comparative genome analysis of test algal strain NIVA-CHL1 (Raphidocelis subcapitata) maintained in microalgal culture collections worldwide |
title_short | Comparative genome analysis of test algal strain NIVA-CHL1 (Raphidocelis subcapitata) maintained in microalgal culture collections worldwide |
title_sort | comparative genome analysis of test algal strain niva-chl1 (raphidocelis subcapitata) maintained in microalgal culture collections worldwide |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7652255/ https://www.ncbi.nlm.nih.gov/pubmed/33166324 http://dx.doi.org/10.1371/journal.pone.0241889 |
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