Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China.
Department of Biology, University of Maryland, College Park, MD, USA.
Mol Ecol Resour. 2021 Jul;21(5):1575-1592. doi: 10.1111/1755-0998.13338. Epub 2021 May 12.
The Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome-level draft genome of S. meridionalis using 69.7-Gb Nanopore long reads and 49.5-Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9-Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed a rod-dominated visual system which was responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of ultraviolet and blue violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow colour vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio led to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of some conserved noncoding elements, which might be associated with the small eyes in catfish. Together, our study provides important clues for the adaptation of the catfish visual system to the nocturnal and benthic lifestyles. The draft genome of S. meridionalis represents a valuable resource for studies of the molecular mechanisms of ecological adaptation.
南方鲇（Silurus meridionalis）是一种夜间活动、底栖的淡水鱼类，分布于长江及其支流。本研究利用 69.7Gb 的纳米孔长读段和 49.5Gb 的 Illumina 短读段构建了南方鲇的染色体水平基因组草图。基因组组装大小为 741.2Mb，contig N50 为 13.19Mb。此外，还使用了 116.4Gb 的 Bionano 和 77.4Gb 的 Hi-C 数据来将 contigs 组装成 scaffolds，进一步组装成 29 条染色体，得到了一个 738.9Mb 的基因组，scaffold N50 为 28.04Mb。共预测到 22965 个蛋白编码基因，其中 22519 个（98.06%）基因具有功能注释。比较基因组学和转录组学分析表明，南方鲇的视觉系统以棒状细胞为主，负责暗视觉。SWS1 和 SWS2 视蛋白缺失导致其缺乏对紫外线和蓝紫光的敏感性。RH1.1、RH1.2 和 RH2 关键氨基酸位点的突变导致光谱调谐良好，适合弱光视觉和窄色视觉。在弱光条件下，棒状细胞光转导基因的表达水平高于锥状细胞，棒状细胞与锥状细胞的比例也较高，导致其具有更高的光学敏感性。此外，对参与眼睛形态发生和发育的基因进行分析发现，一些保守的非编码元件丢失，这可能与鲇鱼的小眼有关。总之，本研究为南方鲇视觉系统适应夜间和底栖生活方式提供了重要线索。南方鲇基因组草图为研究生态适应的分子机制提供了有价值的资源。
