Li Ruihan, Wang Xiaoai, Bian Chao, Gao Zijian, Zhang Yuanwei, Jiang Wansheng, Wang Mo, You Xinxin, Cheng Le, Pan Xiaofu, Yang Junxing, Shi Qiong
College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China.
Front Genet. 2021 Oct 5;12:736500. doi: 10.3389/fgene.2021.736500. eCollection 2021.
An adult , a surface-dwelling golden-line barbel fish, was collected from Maitian river (Kunming City, Yunnan Province, China) for whole-genome sequencing, assembly, and annotation. We obtained a genome assembly of 1.7 Gb with a scaffold N50 of 1.4 Mb and a contig N50 of 24.7 kb. A total of 39,977 protein-coding genes were annotated. Based on a comparative phylogenetic analysis of five species and other five representative vertebrates with published genome sequences, we found that is close to (a cave-restricted species with similar locality). Moreover, the assembled genomes of and other four counterparts were used for a fourfold degenerative third-codon transversion (4dTv) analysis. The recent whole-genome duplication (WGD) event was therefore estimated to occur about 18.1 million years ago. Our results also revealed a decreased tendency of copy number in many important genes related to immunity and apoptosis in cave-restricted species. In summary, we report the first genome assembly of , which provides a valuable genetic resource for comparative studies on cavefish biology, species protection, and practical aquaculture of this potentially economical fish.
从中国云南省昆明市麦天河中采集了一条成年的、生活在水面的金线鲃鱼，用于全基因组测序、组装和注释。我们获得了一个大小为1.7Gb的基因组组装结果，支架N50为1.4Mb，重叠群N50为24.7kb。总共注释了39977个蛋白质编码基因。基于对五个物种以及其他五个具有已发表基因组序列的代表性脊椎动物的比较系统发育分析，我们发现[物种名称]与[另一个物种名称]（一种分布在类似地点的洞穴限制物种）关系密切。此外，[物种名称]和其他四个同类物种的组装基因组用于四重简并第三密码子颠换（4dTv）分析。因此，估计最近的全基因组复制（WGD）事件发生在约1810万年前。我们的结果还揭示了洞穴限制的[物种名称]物种中许多与免疫和细胞凋亡相关的重要基因的拷贝数有下降趋势。总之，我们报告了[物种名称]的首个基因组组装结果，为洞穴鱼类生物学的比较研究、物种保护以及这种具有潜在经济价值鱼类的实际水产养殖提供了宝贵的遗传资源。
