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Four strains, denominated S, K, O, and C, with distinctively different morphologies, have been cultivated commercially since the early 2000s. We previously reported a draft genome of the S-strain. To facilitate studies of seaweed biology for future aquaculture, we here decoded and analyzed genomes of the other three strains (K, O, and C). \nRESULTS: Here we improved the genome of the S-strain (ver. 2, 130 Mbp, 12,999 genes), and decoded the K-strain (135 Mbp, 12,511 genes), the O-strain (140 Mbp, 12,548 genes), and the C-strain (143 Mbp, 12,182 genes). Molecular phylogenies, using mitochondrial and nuclear genes, showed that the S-strain diverged first, followed by the K-strain, and most recently the C- and O-strains. Comparisons of genome architecture among the four strains document the frequent occurrence of inversions. In addition to gene acquisitions and losses, the S-, K-, O-, and C-strains possess 457, 344, 367, and 262 gene families unique to each strain, respectively. Comprehensive Blast searches showed that most genes have no sequence similarity to any entries in the non-redundant protein sequence database, although GO annotation suggested that they likely function in relation to molecular and biological processes and cellular components. \nCONCLUSIONS: Our study compares the genomes of four strains of C. okamuranus and examines their phylogenetic relationships. Due to global environmental changes, including temperature increases, acidification, and pollution, brown algal aquaculture is facing critical challenges. 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Comparative genomics of four strains of the edible brown alga, Cladosiphon okamuranus
https://oist.repo.nii.ac.jp/records/1694
https://oist.repo.nii.ac.jp/records/1694b742426d-8ece-44f8-ab97-62f199e37939
名前 / ファイル | ライセンス | アクション |
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Nishitsuji-2020-Comparative genomics of four s (3.4 MB)
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Creative Commons Attribution 4.0 International(https://creativecommons.org/licenses/by/4.0/)
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Item type | 学術雑誌論文 / Journal Article(1) | |||||
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公開日 | 2020-09-10 | |||||
タイトル | ||||||
言語 | en | |||||
タイトル | Comparative genomics of four strains of the edible brown alga, Cladosiphon okamuranus | |||||
言語 | ||||||
言語 | eng | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Genome decoding | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Cladosiphon strains | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Sets of genes | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Sub-speciation | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Aquaculture | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Pan-genome | |||||
資源タイプ | ||||||
資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||
資源タイプ | journal article | |||||
著者(英) |
Nishitsuji, Koki
× Nishitsuji, Koki× Arimoto, Asuka× Yonashiro, Yoshitaka× Hisata, Kanako× Fujie, Manabu× Kawamitsu, Mayumi× Shoguchi, Eiichi× Satoh, Noriyuki |
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書誌情報 |
en : BMC Genomics 巻 21, 号 1, p. 422, 発行日 2020-06-26 |
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抄録 | ||||||
内容記述タイプ | Other | |||||
内容記述 | BACKGROUND: The brown alga, Cladosiphon okamuranus (Okinawa mozuku), is one of the most important edible seaweeds, and it is cultivated for market primarily in Okinawa, Japan. Four strains, denominated S, K, O, and C, with distinctively different morphologies, have been cultivated commercially since the early 2000s. We previously reported a draft genome of the S-strain. To facilitate studies of seaweed biology for future aquaculture, we here decoded and analyzed genomes of the other three strains (K, O, and C). RESULTS: Here we improved the genome of the S-strain (ver. 2, 130 Mbp, 12,999 genes), and decoded the K-strain (135 Mbp, 12,511 genes), the O-strain (140 Mbp, 12,548 genes), and the C-strain (143 Mbp, 12,182 genes). Molecular phylogenies, using mitochondrial and nuclear genes, showed that the S-strain diverged first, followed by the K-strain, and most recently the C- and O-strains. Comparisons of genome architecture among the four strains document the frequent occurrence of inversions. In addition to gene acquisitions and losses, the S-, K-, O-, and C-strains possess 457, 344, 367, and 262 gene families unique to each strain, respectively. Comprehensive Blast searches showed that most genes have no sequence similarity to any entries in the non-redundant protein sequence database, although GO annotation suggested that they likely function in relation to molecular and biological processes and cellular components. CONCLUSIONS: Our study compares the genomes of four strains of C. okamuranus and examines their phylogenetic relationships. Due to global environmental changes, including temperature increases, acidification, and pollution, brown algal aquaculture is facing critical challenges. Genomic and phylogenetic information reported by the present research provides useful tools for isolation of novel strains. |
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出版者 | ||||||
出版者 | BioMed Central Ltd | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 1471-2164 | |||||
PubMed番号 | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | PMID | |||||
関連識別子 | info:pmid/32586267 | |||||
DOI | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | DOI | |||||
関連識別子 | info:doi/10.1186/s12864-020-06792-8 | |||||
権利 | ||||||
権利情報 | © 2020 The Author(s) | |||||
情報源 | ||||||
関連名称 | https://creativecommons.org/licenses/by/4.0/ | |||||
関連サイト | ||||||
識別子タイプ | URI | |||||
関連識別子 | https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-06792-8 | |||||
著者版フラグ | ||||||
出版タイプ | VoR | |||||
出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 |