Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
Dalian Key Laboratory of Conservation Biology for Endangered Marine Mammals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, China.
Zool Res. 2021 Sep 18;42(5):660-665. doi: 10.24272/j.issn.2095-8137.2021.236.
Flatheads are valuable commercial fish species endemic to the Indo-West Pacific. Due to their economic value and unique biological traits, such as metamorphosis and camouflage, they serve as ideal marine organisms for studies on demersal adaptation and evolution. The brown-spotted flathead ( sp.1) is the most widely distributed in the northwestern Pacific. Despite the lack of a valid scientific name, it has been long recognized and exploited in the marine fisheries of China, Japan, and Korea. In the current study, we applied Illumina, PacBio, and Hi-C sequencing to assemble a chromosome-scale genome for this species. The assembled genome was 660.63 Mb long with a scaffold N50 of 28.65 Mb and 100% of the contigs were anchored onto 24 chromosomes. We predicted 22 743 protein-coding genes, 94.8% of which were functionally annotated. Comparative genomic analyses suggested that sp.1 diverged from its common ancestor with ~88.4 million years ago. The expanded gene families were significantly enriched in immune, biosynthetic, and metabolic pathways. Furthermore, three shared Gene Ontology terms and 377 common positively selected genes were identified between flathead and flatfish species, suggesting that these genes may contribute to demersal adaptation in flatheads. The assembled genomic data provide a valuable molecular resource for further research on the biological and adaptive evolution of flathead species.
平鲷是分布于印度-西太平洋的一种有经济价值的地方特有鱼类。由于其具有经济价值和独特的生物学特征，如变态和伪装，因此它们是研究底栖适应和进化的理想海洋生物。棕斑平鲷（sp.1）是西北太平洋分布最广的平鲷。尽管缺乏有效的科学名称，但在中国、日本和韩国的海洋渔业中，这种鱼类早已被认识和开发。在本研究中，我们应用 Illumina、PacBio 和 Hi-C 测序技术，为该物种组装了一个染色体级别的基因组。组装的基因组大小为 660.63 Mb，支架 N50 为 28.65 Mb，100%的 contigs锚定在 24 条染色体上。我们预测了 22743 个蛋白质编码基因，其中 94.8%具有功能注释。比较基因组分析表明，sp.1 与其共同祖先分化的时间约为 8840 万年前。扩展的基因家族在免疫、生物合成和代谢途径中显著富集。此外，在平鲷和平鱼物种之间鉴定出三个共同的基因本体论术语和 377 个共同的阳性选择基因，这表明这些基因可能有助于平鲷的底栖适应。组装的基因组数据为进一步研究平鲷物种的生物学和适应性进化提供了有价值的分子资源。
