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). 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. 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.

中文翻译：

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四种食用褐藻 Cladosiphon okamuranus 菌株的比较基因组学。


褐藻 Cladosiphon okamuranus（冲绳海蕴）是最重要的食用海藻之一，主要在日本冲绳种植供市场销售。自 2000 年代初期以来，有四种菌株，分别命名为 S、K、O 和 C，具有明显不同的形态。我们之前报道了 S 株的基因组草图。为了促进未来水产养殖的海藻生物学研究，我们在这里解码并分析了其他三种菌株（K、O 和 C）的基因组。在这里，我们改进了 S 株（版本 2，130 Mbp，12,999 个基因）的基因组，并解码了 K 株（135 Mbp，12,511 个基因）、O 株（140 Mbp，12,548 个基因）和C 菌株（143 Mbp，12,182 个基因）。使用线粒体和核基因进行的分子系统发育表明，S 株首先分化，其次是 K 株，最后是 C 株和 O 株。四种菌株之间基因组结构的比较记录了倒位的频繁发生。除了基因获得和丢失之外，S、K、O 和 C 菌株分别拥有每个菌株特有的 457、344、367 和 262 个基因家族。全面的 Blast 搜索表明，大多数基因与非冗余蛋白质序列数据库中的任何条目都没有序列相似性，尽管 GO 注释表明它们可能与分子和生物过程以及细胞成分相关。我们的研究比较了 C. okamuranus 四种菌株的基因组，并检查了它们的系统发育关系。由于全球环境变化，包括气温升高、酸化和污染，褐藻养殖面临严峻挑战。 本研究报告的基因组和系统发育信息为分离新菌株提供了有用的工具。