Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, China; Wuhan Xianfeng Aquaculture Technology Co. Ltd, Wuhan 430207, China.
State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
Comp Biochem Physiol Part D Genomics Proteomics. 2021 Dec;40:100910. doi: 10.1016/j.cbd.2021.100910. Epub 2021 Sep 7.
Determining the sex and controlling the sex ratio are essential aspects of fish genetics that can assist in developing successful fish breeding programs. High quality genome assembly and annotations are prerequisites to determine sex-specific genes and their expression. In addition, analysis of resequencing data can identify genomic difference between male and female fishes. In this study, we performed chromosome-level genome assembly in female Ancherythroculter nigrocauda fish having low heterozygosity using PacBio reads. High-throughput chromatin conformation capture (HiC) yielded a genome of size 1054.05 Mb, with a contig N50 length of 3.40 Mb and a scaffold N50 length of 42.68 Mb. In addition, we sequenced 5 female and 5 male A. nigrocauda samples and identified sex-specific regions on LG20 Furthermore, diet-specific amino acid mutation were found on 582 genes between herbivorous and carnivorous fishes, with 26 of them exhibiting significantly different expression patterns in the liver tissue of these two types of fishes. The chromosome-level genome assembly of A. nigrocauda provides valuable resources for conducting in-depth comparative genomic studies with immense applications in fish genetic breeding and farming. Similarly, the diet-specific amino acid mutations are useful in the breeding of new strains of carnivorous fishes with an herbivorous diet.
确定鱼类的性别和控制性别比例是鱼类遗传学的重要方面，可以帮助开发成功的鱼类养殖计划。高质量的基因组组装和注释是确定性别特异性基因及其表达的前提。此外，重测序数据分析可以识别雌雄鱼类之间的基因组差异。在这项研究中，我们使用 PacBio reads 对杂合度低的雌性云南光唇鱼进行了染色体水平的基因组组装。高通量染色质构象捕获（HiC）产生了大小为 1054.05 Mb 的基因组，其 contig N50 长度为 3.40 Mb，scaffold N50 长度为 42.68 Mb。此外，我们对 5 条雌性和 5 条雄性 A. nigrocauda 样本进行了测序，并在 LG20 上鉴定了性别特异性区域。此外，在草食性和肉食性鱼类之间的 582 个基因上发现了特定于饮食的氨基酸突变，其中 26 个基因在这两种鱼类的肝脏组织中表现出显著不同的表达模式。云南光唇鱼的染色体水平基因组组装为进行深入的比较基因组研究提供了有价值的资源，在鱼类遗传育种和养殖方面具有广泛的应用。同样，饮食特异性氨基酸突变可用于培育具有草食性饮食的新型肉食性鱼类。
