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.

中文翻译：

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南部鲶鱼（silurus meridionalis）的染色体水平组装提供了对夜间和底栖生活方式的视觉适应的见解

南鲶（Silurus meridionalis）是长江及其支流特有的夜间和底栖淡水鱼类。在这项研究中，我们构建了S染色体水平的基因组草图。子午线使用 69.7-Gb Nanopore 长读取和 49.5-Gb Illumina 短读取。基因组组装大小为 741.2 Mb，contig N50 为 13.19 Mb。额外的 116.4 Gb Bionano 和 77.4 Gb Hi-C 数据用于将重叠群组装到支架中，并进一步组装到 29 条染色体中，从而产生 738.9-Mb 的基因组，支架 N50 为 28.04 Mb。从基因组中总共预测了 22,965 个蛋白质编码基因，其中 22,519 (98.06%) 个基因进行了功能注释。比较基因组和转录组分析揭示了一个以杆为主的视觉系统，它负责暗视觉。视锥视蛋白 SWS1 和 SWS2 的缺失导致缺乏紫外线和蓝紫色敏感性。RH1.1、RH1.2 和 RH2 关键氨基酸位点的突变导致光谱调谐有利于弱光视觉和窄色觉。杆状光转导基因的表达水平高于视锥基因和更高的视杆锥比导致在昏暗的光照条件下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的分析揭示了一些保守的非编码元件的丢失，这可能与鲶鱼的小眼睛有关。总之，我们的研究为鲶鱼视觉系统适应夜间和底栖生活方式提供了重要线索。基因组草图 这可能与鲶鱼的小眼睛有关。总之，我们的研究为鲶鱼视觉系统适应夜间和底栖生活方式提供了重要线索。基因组草图 这可能与鲶鱼的小眼睛有关。总之，我们的研究为鲶鱼视觉系统适应夜间和底栖生活方式提供了重要线索。基因组草图小号。meridionalis是研究生态适应分子机制的宝贵资源。