High-quality genome assembly and transcriptome of Ancherythroculter nigrocauda, an endemic Chinese cyprinid species
High-quality genome assembly and transcriptome of Ancherythroculter nigrocauda, an endemic Chinese cyprinid species
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中国特有鲤鱼Ancherythroculter nigrocauda的高质量基因组组装和转录组
DOI：
10.1111/1755-0998.13158
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发表时间：
2020
影响因子：
7.7
通讯作者：
Dai Fang-Yin
中科院分区：
文献类型：
--
作者：
Zhang Hua-Hao;Xu Min-Rui-Xuan;Wang Ping-Lan;Zhu Zhi-Guo;Nie Cheng-Feng;Xiong Xiao-Min;Wang Le;Xie Zhen-Zhen;Wen Xu;Zeng Qing-Xiang;Zhang Xiao-Gu;Dai Fang-Yin
黑尾近红翘嘴鱼（Ancherythroculter nigrocauda）是我国长江上游特有的鲤科鱼类，是长江上游重要的养殖和经济鱼种。由于过度捕捞、水坝建设和水污染，它也是一种受威胁的物种。在这项研究中，A.报道并使用PacBio测序和Hi-C技术构建黑尾。1.04-Gb的A. nigrocauda包含2，403个重叠群，N50长度为3.12 Mb。然后，将1，297个重叠群组装成24条染色体，这代表了所有重叠群的54.0%和基因组核苷酸碱基总含量的97.2%。结合来自10种组织的转录组数据，在34，414个预测的蛋白质编码基因中，有27，042个（78.5%）基因被功能注释。有趣的是，许多正选择基因和扩展的基因家族在大脑中的高表达表明，这些基因可能在大脑发育中发挥重要作用。黑尾。最后，我们发现了10，732个基因的组织特异性表达。功能分析表明，它们主要由与（a）环境信息处理、（B）循环系统和（c）发育相关的基因组成，这表明它们可能在适应不同环境和A的发育中起重要作用。黑尾。本研究获得的高质量基因组不仅为今后的A. nigrocauda种群和保护，但也是一个重要的资源，为进一步的功能基因组学研究的鱼类。
Ancherythroculter nigrocaudais a cyprinid fish endemic of the upper reaches of the Yangtze River in China, where it is an important aquaculture and commercial species. It is also a threatened species as a result of overfishing, dam construction and water pollution. In this study, a chromosome‐level genome assembly ofA. nigrocaudais reported and built using PacBio sequencing and the Hi‐C technology. The 1.04‐Gb sequenced genome ofA. nigrocaudacontained 2,403 contigs, with an N50 length of 3.12 Mb. Then, 1,297 contigs, which represented 54.0% of all contigs and 97.2% of the whole content of the genome nucleotide base, were assembled into 24 chromosomes. Combined with transcriptome data from 10 tissues, 27,042 (78.5%) genes were functionally annotated out of 34,414 predicted protein‐coding genes. Interestingly, high expression of many positively selected genes and expanded gene families in the brain suggested that these genes might play important roles in brain development inA. nigrocauda. Finally, we found tissue‐specific expression of 10,732 genes. Functional analyses showed that they were mainly composed of genes related to (a) environmental information processing, (b) the circulatory system, and (c) development, suggesting they might be important for adaptation to different environments and for development ofA. nigrocauda. The high‐quality genome obtained in this study not only provides a valuable genomic resource for future studies ofA. nigrocaudapopulations and conservation, but is also an important resource for further functional genomics studies of fishes.