Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai'an 223300, China.
Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
DNA Res. 2022 Jun 25;29(4). doi: 10.1093/dnares/dsac028.
Pseudobagrus ussuriensis is an aquaculture catfish with significant sexual dimorphism. In this study, a chromosome-level genome with a size of 741.97 Mb was assembled for female P. ussuriensis. A total of 26 chromosome-level contigs covering 97.34% of the whole-genome assembly were obtained with an N50 of 28.53 Mb and an L50 of 11. A total of 24,075 protein-coding genes were identified, with 91.54% (22,039) genes being functionally annotated. Based on the genome assembly, four chromosome evolution clusters of catfishes were identified and the formation process of P. ussuriensis chromosomes was predicted. A total of 55 sex-related quantitative trait loci (QTLs) with a phenotypic variance explained value of 100% were located on chromosome 8 (chr08). The QTLs and other previously identified sex-specific markers were located in a sex-determining region of 16.83 Mb (from 6.90 to 23.73 Mb) on chr08, which was predicted as the X chromosome. The sex-determining region comprised 554 genes, with 135 of which being differently expressed between males and females/pseudofemales, and 16 candidate sex-determining genes were screened out. The results of this study provided a useful chromosome-level genome for genetic, genomic and evolutionary studies of P. ussuriensis, and also be useful for further studies on sex-determination mechanism analysis and sex-control breeding of this fish.
乌苏里拟鲿是一种具有显著性二型的水产养殖鲶鱼。本研究组装了一个大小为 741.97 Mb 的雌性乌苏里拟鲿染色体水平基因组。共获得 26 条染色体水平的 contigs，覆盖整个基因组组装的 97.34%，N50 为 28.53 Mb，L50 为 11。共鉴定出 24075 个蛋白质编码基因，其中 91.54%（22039 个）基因具有功能注释。基于基因组组装，鉴定出了 4 个鲶鱼染色体进化簇，并预测了乌苏里拟鲿染色体的形成过程。总共定位到 55 个与性别相关的数量性状位点（QTLs），这些 QTLs的表型方差解释值为 100%，位于第 8 号染色体（chr08）上。这些 QTLs 和其他先前鉴定的性别特异性标记位于 chr08 上 16.83 Mb 的性别决定区域（从 6.90 到 23.73 Mb）内，该区域被预测为 X 染色体。性别决定区域包含 554 个基因，其中 135 个基因在雄性和雌性/假雌性之间表达不同，筛选出 16 个候选性别决定基因。本研究结果为乌苏里拟鲿的遗传、基因组和进化研究提供了一个有用的染色体水平基因组，也为进一步研究该鱼类的性别决定机制分析和性别控制育种提供了帮助。
