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<p><i>Rhinogobio ventralis</i>, a critically endangered freshwater fish endemic to the upper Yangtze River, holds significant ecological and economic value. Here, we present a high-quality chromosome-level genome assembly of <i>R. ventralis</i>. Using a combination of PacBio HiFi long-read sequencing (&gt;99% single-read accuracy), DNBSEQ-T7 short-read sequencing (95.7% of bases ≥ Q30), and Hi-C scaffolding, we assembled a 1,039.34 Mb genome comprising 478 contigs with a contig N50 of 18.1 Mb. Hi-C data anchored 97.9% of the assembled sequence onto 25 chromosomes. The final assembly is highly complete (BUSCO completeness 96.6%) and accurate (QV 48.22). Repetitive elements account for 63.44% of the genome, with DNA transposons alone representing 42.31%. We predicted 23,246 protein-coding genes, of which 98.6% have functional annotations. This high-quality genome assembly provides a valuable resource for future studies on the genetics, adaptive evolution, and conservation of <i>R. ventralis</i> and other endangered freshwater fishes.</p>

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Chromosome-level genome assembly and annotation of the Rhinogobio ventralis, an endangered endemic fish from the Yangtze River

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年3月6日

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  • Yan Zhao,
  • Xingbing Wu,
  • Weixin Zheng,
  • Xiaoli Li,
  • Yongjiu Zhu,
  • Tingbing Zhu,
  • Xuemei Li

摘要

Rhinogobio ventralis, a critically endangered freshwater fish endemic to the upper Yangtze River, holds significant ecological and economic value. Here, we present a high-quality chromosome-level genome assembly of R. ventralis. Using a combination of PacBio HiFi long-read sequencing (>99% single-read accuracy), DNBSEQ-T7 short-read sequencing (95.7% of bases ≥ Q30), and Hi-C scaffolding, we assembled a 1,039.34 Mb genome comprising 478 contigs with a contig N50 of 18.1 Mb. Hi-C data anchored 97.9% of the assembled sequence onto 25 chromosomes. The final assembly is highly complete (BUSCO completeness 96.6%) and accurate (QV 48.22). Repetitive elements account for 63.44% of the genome, with DNA transposons alone representing 42.31%. We predicted 23,246 protein-coding genes, of which 98.6% have functional annotations. This high-quality genome assembly provides a valuable resource for future studies on the genetics, adaptive evolution, and conservation of R. ventralis and other endangered freshwater fishes.