CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
Mol Ecol Resour. 2022 Jul;22(5):1892-1905. doi: 10.1111/1755-0998.13582. Epub 2022 Jan 21.
The cottids (Cottidae) are a taxonomically diverse and ecologically important component of many marine and freshwater ecosystems. Despite recent breakthroughs in long-read sequencing, high quality genomic resources are still limited for studies of ecological and evolutionary processes in cottids. Here, we generated a high-quality, chromosome-scale genome assembly (521.26 Mb) of the catadromous roughskin sculpin (Trachidermus fasciatus Heckel) with a contig N50 of 2.93 Mb and a scaffold N50 of 24.06 Mb. Approximately 21.97% of the genome was composed of repetitive elements. A total of 21,872 protein-coding genes were predicted, of which 19,900 genes (90.98%) were functionally annotated. Phylogenetic analysis supported the validity of Scorpaenoidei and Cottioidei as two suborders of the Perciformes. Chromosome-scale collinearity analyses identified four chromosome fusions leading to the reduction of chromosome number in T. fasciatus. Gene families related to cell apoptosis and cell death were expanded and those related to immune system were contracted, suggesting that these gene families might be relevant to a host of phenotypic differences between T. fasciatus and other teleosts. Gene families associated with osmoregulation were also expanded, which might be associated with its catadromous life history. A total of 50 aging-associated genes were found to be under positive selection, which might be associated with the short lifespan of T. fasciatus. The high-quality genome assembly and annotation will promote researches into the evolution of catadromous life history and short lifespan for T. fasciatus and facilitate comparative genomic studies of cottids in the near future.
鲈形目鱼类包括多种具有不同生态特征的物种，是许多海洋和淡水生态系统的重要组成部分。尽管近年来长读测序技术取得了突破，但高质量的基因组资源仍然有限，无法满足对鲈形目鱼类生态和进化过程的研究需求。本研究以洄游性的糙皮鲉（Trachidermus fasciatus Heckel）为研究对象，生成了一个高质量的染色体水平基因组组装（521.26 Mb），其 Contig N50 为 2.93 Mb，Scaffold N50 为 24.06 Mb。基因组中约 21.97%由重复序列组成。共预测到 21872 个蛋白编码基因，其中 19900 个基因（90.98%）具有功能注释。系统发育分析支持将 Scorpaenoidei 和 Cottioidei 作为鲈形目两个亚目。染色体水平的共线性分析鉴定出导致糙皮鲉染色体数减少的四次染色体融合事件。与细胞凋亡和细胞死亡相关的基因家族发生扩张，与免疫系统相关的基因家族发生收缩，这表明这些基因家族可能与糙皮鲉和其他硬骨鱼之间的一系列表型差异有关。与渗透压调节相关的基因家族也发生扩张，这可能与糙皮鲉的洄游生活史有关。共发现 50 个与衰老相关的基因受到正选择，这可能与糙皮鲉的短寿命有关。该高质量基因组组装和注释将促进对糙皮鲉洄游生活史和短寿命进化的研究，并为未来开展鲈形目鱼类的比较基因组学研究提供便利。
