College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China.
Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, 021000, Inner Mongolia, China.
Sci Data. 2022 Sep 1;9(1):535. doi: 10.1038/s41597-022-01648-0.
Chanodichthys erythropterus is a fierce carnivorous fish widely found in East Asian waters. It is not only a popular food fish in China, it is also a representative victim of overfishing. Genetic breeding programs launched to meet market demands urgently require high-quality genomes to facilitate genomic selection and genetic research. In this study, we constructed a chromosome-level reference genome of C. erythropterus by taking advantage of long-read single-molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi-C. The 1.085 Gb C. erythropterus genome was assembled from 132 Gb of Nanopore sequence. The assembled genome represents 98.5% completeness (BUSCO) with a contig N50 length of 23.29 Mb. The contigs were clustered and ordered onto 24 chromosomes covering roughly 99.49% of the genome assembly with Hi-C data. Additionally, 33,041 (98.0%) genes were functionally annotated from a total of 33,706 predicted protein-coding sequences by combining transcriptome data from seven tissues. This high-quality assembled genome will be a precious resource for future molecular breeding and functional genomics research of C. erythropterus.
赤眼鳟是一种广泛分布于东亚水域的凶猛肉食性鱼类。它不仅是中国受欢迎的食用鱼类，也是过度捕捞的代表性受害者。为满足市场需求而推出的遗传育种计划迫切需要高质量的基因组，以促进基因组选择和遗传研究。在这项研究中，我们利用长读长单分子测序和牛津纳米孔技术（ONT）和 Hi-C 的从头组装，构建了赤眼鳟的染色体水平参考基因组。该 1.085Gb 的赤眼鳟基因组由 132Gb 的纳米孔序列组装而成。组装的基因组具有 98.5%的完整性（BUSCO），其 contig N50 长度为 23.29Mb。利用 Hi-C 数据，将 contigs 聚类并排列到 24 条染色体上，覆盖了基因组组装的大约 99.49%。此外，通过结合来自七个组织的转录组数据，总共预测了 33706 个编码蛋白质的序列，其中有 33041 个（98.0%）基因被功能注释。这个高质量的组装基因组将成为赤眼鳟未来分子育种和功能基因组学研究的宝贵资源。
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