First Institute of Oceanography, Ministry of Natural Resources, Qingdao, Shandong, China.
Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, China.
Genome Biol Evol. 2021 Feb 3;13(2). doi: 10.1093/gbe/evaa246.
Argyrosomus japonicus is an economically and ecologically important fish species in the family Sciaenidae with a wide distribution in the world's oceans. Here, we report a high-quality, chromosome-level genome assembly of A. japonicus based on PacBio and Hi-C sequencing technology. A 673.7-Mb genome containing 282 contigs with an N50 length of 18.4 Mb was obtained based on PacBio long reads. These contigs were further ordered and clustered into 24 chromosome groups based on Hi-C data. In addition, a total of 217.2 Mb (32.24% of the assembled genome) of sequences were identified as repeat elements, and 23,730 protein-coding genes were predicted based on multiple approaches. More than 97% of BUSCO genes were identified in the A. japonicus genome. The high-quality genome assembled in this work not only provides a valuable genomic resource for future population genetics, conservation biology and selective breeding studies of A. japonicus but also lays a solid foundation for the study of Sciaenidae evolution.
日本红娘鱼是石首鱼科中一种具有重要经济和生态意义的鱼类，分布广泛。本研究基于 PacBio 和 Hi-C 测序技术，报道了日本红娘鱼的高质量染色体水平基因组组装。利用 PacBio 长读长，获得了包含 282 个 contigs 的 673.7-Mb 基因组，N50 长度为 18.4 Mb。这些 contigs 进一步基于 Hi-C 数据进行了排序和聚类，形成 24 个染色体组。此外，共鉴定出 217.2 Mb（组装基因组的 32.24%）的序列为重复元件，基于多种方法预测了 23730 个蛋白质编码基因。在日本红娘鱼基因组中鉴定出超过 97%的 BUSCO 基因。本研究组装的高质量基因组不仅为未来日本红娘鱼的群体遗传学、保护生物学和选择性育种研究提供了有价值的基因组资源，也为石首鱼科的进化研究奠定了坚实的基础。
