Han Zhaofang, Li Wanbo, Zhu Wen, Sun Sha, Ye Kun, Xie Yangjie, Wang Zhiyong
Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College Jimei University Xiamen China.
Laboratory for Marine Fisheries Science and Food Production Processes Qingdao National Laboratory for Marine Science and Technology Qingdao China.
Ecol Evol. 2018 Dec 11;9(1):568-575. doi: 10.1002/ece3.4778. eCollection 2019 Jan.
Yellow drum () is an important fish species in capture fishery and aquaculture in East Asia. We herein report the first and near-complete genome assembly of an ultra-homologous gynogenic female yellow drum using Illumina short sequencing reads. In summary, a total of 154.2 Gb of raw reads were generated via whole-genome sequencing and were assembled to 565.3 Mb genome with a contig N size of 50.3 kb and scaffold N size of 2.2 Mb (BUSCO completeness of 97.7%), accounting for 97.3%-98.6% of the estimated genome size of this fish. We further identified 22,448 genes using combined methods of ab initio prediction, RNAseq annotation, and protein homology searching, of which 21,614 (96.3%) were functionally annotated in NCBI nr, trEMBL, SwissProt, and KOG databases. We also investigated the nucleotide diversity (around 1/390) of aquacultured individuals and found the genetic diversity of the aquacultured population decreased due to inbreeding. Evolutionary analyses illustrated significantly expanded and extracted gene families, such as myosin and sodium: neurotransmitter symporter (SNF), could help explain swimming motility of yellow drum. The presented genome will be an important resource for future studies on population genetics, conservation, understanding of evolutionary history and genetic breeding of the yellow drum and other species.
黄姑鱼（）是东亚海洋捕捞和水产养殖中的重要鱼类。在此，我们报告了首例利用Illumina短测序reads对超同源雌核发育黄姑鱼进行的近乎完整的基因组组装。总的来说，通过全基因组测序共产生了154.2Gb的原始reads，并组装成了一个565.3Mb的基因组，其重叠群N50大小为50.3kb，支架N50大小为2.2Mb（BUSCO完整性为97.7%），占该鱼类估计基因组大小的97.3%-98.6%。我们进一步使用从头预测、RNAseq注释和蛋白质同源性搜索的组合方法鉴定了22448个基因，其中21614个（96.3%）在NCBI nr、trEMBL、SwissProt和KOG数据库中得到了功能注释。我们还研究了养殖个体的核苷酸多样性（约为1/390），发现由于近亲繁殖，养殖群体的遗传多样性有所下降。进化分析表明，显著扩张和特异的基因家族，如肌球蛋白和钠：神经递质转运体（SNF），有助于解释黄姑鱼的游泳运动能力。所展示的基因组将成为未来黄姑鱼及其他物种群体遗传学、保护、进化历史理解和遗传育种研究的重要资源。
