Shen Qi, Wu Junjie, Yang Chunxiang, Sheng Qiang, Xu Mei, Yi Shaokui, Song Jianyu
School of Life Sciences, Huzhou University, Huzhou, 313000, China.
Yunnan Institute of Fishery Sciences Research, Kunming, 650111, China.
Sci Data. 2025 Jul 11;12(1):1196. doi: 10.1038/s41597-025-05547-y.
Barbodes wynaadensis, a unique cyprinid species native to Yunnan Province in China, stands out as an allotetraploid (AABB) fish with a complex evolutionary history. Leveraging a multi-platform sequencing strategy combining MGI short-read, PacBio long-read, and Hi-C scaffolding technologies, we assembled the first chromosome-level genome for B. wynaadensis. The final assembled genome spans 1.76 Gb in length with a contig N50 of 33.53 Mb, demonstrating high assembly continuity. Hi-C scaffolding enabled the reconstruction of 50 pseudochromosomes, representing 99.94% of the total genome assembly. Genome annotation identified 46,121 protein-coding genes, with a functional annotation rate of 99.76%. Repetitive elements constituted 48.26% of the genomic sequences, including lineage-specific expansions of DNA transposons (29.26%) and LTRs (6.36%). This high-quality assembly resolves challenges in polyploid genome reconstruction and provides a critical resource for investigating Cyprinidae evolution, particularly subgenome divergence and adaptation. The dataset also enables practical applications, such as molecular marker development for population monitoring, supporting conservation efforts for this threatened endemic species amid habitat degradation in the Nujiang River basin.
温氏无须魮是中国云南省特有的鲤科鱼类，是一种具有复杂进化历史的异源四倍体（AABB）鱼类。我们采用了一种结合华大基因短读长、PacBio长读长和Hi-C支架技术的多平台测序策略，成功组装了温氏无须魮的首个染色体水平基因组。最终组装的基因组长度为1.76 Gb，重叠群N50为33.53 Mb，显示出高组装连续性。Hi-C支架技术实现了50条假染色体的重建，占基因组组装总量的99.94%。基因组注释鉴定出46121个蛋白质编码基因，功能注释率为99.76%。重复元件占基因组序列的48.26%，包括DNA转座子（29.26%）和长末端重复序列（LTRs，6.36%）的谱系特异性扩增。这种高质量的组装解决了多倍体基因组重建中的挑战，并为研究鲤科鱼类的进化，特别是亚基因组分化和适应性提供了关键资源。该数据集还具有实际应用价值，例如用于种群监测的分子标记开发，有助于在怒江流域栖息地退化的情况下对这种濒危特有物种进行保护。
