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<p><i>Xenocypris davidi</i> is a benthic fish species widely distributed in the water systems south of the Yellow River in China, playing a significant role in aquatic ecosystems. Despite its ecological and economic importance, genomic resources for <i>X. davidi</i> are limited, hindering a comprehensive understanding of its evolutionary adaptations and genetic improvements. This study presents the first chromosome-level genome assembly of <i>X. davidi</i>, utilizing PacBio long-reads, Illumina short reads, and Hi-C sequencing data. The genome assembly spans 1.05 Gb with a scaffold N50 length of 33.99 Mb, and 95.12% of the genome sequence was successfully anchored onto 24 pseudochromosomes. We identified 27,360 protein-coding genes, of which 26,672 were functionally annotated. This genome sequence provides a valuable resource for exploring the molecular basis of agronomic traits in <i>X. davidi</i> and will facilitate its genetic enhancement.</p>

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Chromosome-scale assembly of the Xenocypris davidi using PacBio HiFi reads and Hi-C technologies

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年3月18日

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  • Tiezhu Yang,
  • Liangjie Zhao,
  • Chaoqun Su,
  • Xusheng Guo,
  • Xinliang Peng,
  • Shijie Yang,
  • Gaoyou Yao

摘要

Xenocypris davidi is a benthic fish species widely distributed in the water systems south of the Yellow River in China, playing a significant role in aquatic ecosystems. Despite its ecological and economic importance, genomic resources for X. davidi are limited, hindering a comprehensive understanding of its evolutionary adaptations and genetic improvements. This study presents the first chromosome-level genome assembly of X. davidi, utilizing PacBio long-reads, Illumina short reads, and Hi-C sequencing data. The genome assembly spans 1.05 Gb with a scaffold N50 length of 33.99 Mb, and 95.12% of the genome sequence was successfully anchored onto 24 pseudochromosomes. We identified 27,360 protein-coding genes, of which 26,672 were functionally annotated. This genome sequence provides a valuable resource for exploring the molecular basis of agronomic traits in X. davidi and will facilitate its genetic enhancement.