Chromosome-level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles
Chromosome-level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles
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南方鲶鱼（南方鲶）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
DOI：
10.1111/1755-0998.13338
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发表时间：
2021
影响因子：
7.7
通讯作者：
Zhang Yaoguang
中科院分区：
文献类型：
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作者：
Zheng Shuqing;Shao Feng;Tao Wenjing;Liu Zhilong;Long Juan;Wang Xiaoshuang;Zhang Shuai;Zhao Qingyuan;Carleton Karen L.;Kocher Thomas D.;Jin Li;Wang Zhijian;Peng Zuogang;Wang Deshou;Zhang Yaoguang
南方鲇是长江及其支流特有的夜行性底栖淡水鱼类。在这项研究中，我们使用69.7-Gb Nanopore长读段和49.5-Gb Illumina短读段构建了一个染色体水平的沙门氏菌基因组草图。基因组组装体的大小为741.2 Mb，重叠群N50为13.19 Mb。应用另外116.4 Gb的Bionano和77.4 Gb的Hi-C数据将重叠群组装到支架中，并进一步组装到29条染色体中，得到738.9-Mb基因组，支架N50为28.04 Mb。从基因组中预测了总共22，965个蛋白质编码基因，其中22，519个（98.06%）基因进行了功能注释。比较基因组学和转录组学分析揭示了一个杆主导的视觉系统，这是暗视觉的原因。视锥蛋白SWS 1和SWS 2的缺乏导致缺乏紫外和蓝紫敏感性。在RH1.1、RH1.2和RH 2的关键氨基酸位点处的突变导致对昏暗光视觉和窄色觉良好的光谱调谐。视杆细胞光转导基因的表达水平高于视锥细胞基因的表达水平，且视杆细胞与视锥细胞的比例越高，在弱光条件下的光学敏感度越高。此外，对与眼睛形态发生和发育有关的基因的分析显示，一些保守的非编码元件丢失，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。该菌的基因组草图为研究其生态适应的分子机制提供了宝贵的资源。
The Southern catfish (Silurusmeridionalis) 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 ofS.meridionalisusing 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 ofS.meridionalisrepresents a valuable resource for studies of the molecular mechanisms of ecological adaptation.