Liu Dong, Wang Xiaolong, Lü Jifa, Zhu Yijing, Jian Yuxia, Wang Xue, Gao Fengxiang, Li Li, Hu Fawen
Laboratory of Benthic Fisheries Aquaculture and Enhancement, Shandong Key Laboratory of Intelligent Marine Ranch (Under Preparation), Marine Science Research Institute of Shandong Province (National Oceanographic Center, Qingdao), Qingdao 266104, China.
Animals (Basel). 2025 Mar 10;15(6):782. doi: 10.3390/ani15060782.
, also commonly called "Fat Greenling", is highly valued as an important commercial fish due to its extremely delicious flesh. However, the absence of a genomic resource has limited our understanding of its genetic characteristics and hindered artificial breeding efforts. In this study, we performed Illumina paired-end sequencing of , generating a total of 73.19 Gb of clean data. Based on K-mer analysis, the genome size was estimated to be 679.23 Mb, with a heterozygosity rate of 0.68% and a repeat sequence proportion of 43.60%. De novo genome assembly using SOAPdenovo2 resulted in a draft genome size of 723.31 Mb, with the longest sequence length being 86.24 Kb. Additionally, the mitochondrial genome was also assembled, which was 16,513 bp in size, with a GC content of 47.20%. Minisatellites were the most abundant tandem repeats in the genome, followed by microsatellites. In the phylogenetic tree, was placed within a well-supported clade (bootstrap support = 100%) that included , , , and . PSMC analysis revealed that underwent a population bottleneck during the Pleistocene, peaking around 500 thousand years ago (Kya) and declining to a minimum during the Last Glacial Period (~70-15 Kya), with no significant recovery observed by ~10 Kya. This study was a comprehensive genome survey analysis of , providing insights into its genomic characteristics and population dynamics.
，也通常被称为“肥绿鳍鱼”，因其肉质极其鲜美而被视为重要的商业鱼类。然而，缺乏基因组资源限制了我们对其遗传特征的了解，并阻碍了人工养殖的努力。在本研究中，我们对 进行了Illumina双末端测序，共产生了73.19 Gb的干净数据。基于K-mer分析，估计基因组大小为679.23 Mb，杂合率为0.68%，重复序列比例为43.60%。使用SOAPdenovo2进行从头基因组组装，得到的基因组草图大小为723.31 Mb，最长序列长度为86.24 Kb。此外，还组装了线粒体基因组，其大小为16,513 bp，GC含量为47.20%。微卫星是 基因组中最丰富的串联重复序列，其次是微卫星。在系统发育树中， 被置于一个得到充分支持的分支内（自展支持率 = 100%），该分支包括 、 、 和 。PSMC分析表明， 在更新世经历了种群瓶颈，在约50万年前（Kya）达到峰值，在末次冰期（约70 - 15 Kya）降至最低，到约10 Kya时未观察到显著恢复。本研究是对 的全面基因组调查分析，为其基因组特征和种群动态提供了见解。
