A high-quality chromosome-level genome of the endangered roughskin sculpin provides insights into its evolution and adaptation
A high-quality chromosome-level genome of the endangered roughskin sculpin provides insights into its evolution and adaptation
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DOI：
10.1111/1755-0998.13582
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发表时间：
2022-01-21
影响因子：
7.7
通讯作者：
Liu，Jin-Xian
中科院分区：
文献类型：
--
作者：
Xue，Dong-Xiu;Xing，Teng-Fei;Liu，Jin-Xian
科是许多海洋和淡水生态系统的分类多样性和重要的生态组成部分。尽管最近在长阅读测序方面取得了突破性进展，但高质量的基因组资源在研究棉铃虫的生态和进化过程方面仍然有限。在这里，我们产生了一个高质量的，染色体规模的基因组组件(521.26 Mb)，其中重叠群N50为2.93Mb，支架N50为24.06Mb。约21.97%的基因组由重复元件组成。共预测了21,872个蛋白质编码基因，其中19,900个基因(90.98%)得到了功能注释。系统发育分析支持Scorpaenoidei和Cottioidei作为贻贝形目的两个亚目。染色体尺度共线分析鉴定出四种染色体融合导致扁尾线虫染色体数目减少。与细胞凋亡和细胞死亡相关的基因家族被扩展，而与免疫系统相关的基因家族被收缩，这表明这些基因家族可能与筋膜螺旋体和其他硬骨鱼之间的一系列表型差异有关。与渗透调节相关的基因家族也得到了扩展，这可能与其退行性生活史有关。共有50个与衰老相关的基因处于正选择状态，这可能与扁平线虫的短寿命有关。高质量的基因组拼接和注释将促进对扁平线虫退化生活史和短寿命进化的研究，并有助于在不久的将来进行比较基因组学研究。
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 fasciatusHeckel) 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 inT.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 betweenT.fasciatusand 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 ofT.fasciatus. The high‐quality genome assembly and annotation will promote researches into the evolution of catadromous life history and short lifespan forT.fasciatusand facilitate comparative genomic studies of cottids in the near future.