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<p><i>Triplophysa pappenheimi</i>, an ecologically important species within the plateau freshwater ecosystem, predominantly inhabits the rapids of the upper Yellow River, its tributaries, and associated lakes, playing a crucial role in maintaining local aquatic biodiversity and serving as a model for plateau fish adaptation studies. In this study, we utilized a combination of Illumina short-read sequencing, PacBio HiFi long-read sequencing, and Hi-C technology to generate the first high-quality, chromosome-level genome assembly of <i>T. pappenheimi</i>. The assembled genome spans 626.33 Mb, organized into 25 pseudochromosomes, with a scaffold N50 of 24.41 Mb. We annotated 24,952 genes, representing 98.82% of the predicted protein-coding genes. In addition, we used GetOrganelle v1.7.7.1 to isolate and assemble the complete mitochondrial genome from the Illumina sequencing data, with a total length of 16,574 bp, and successfully achieved circularization. This high-quality genome assembly provides a valuable genomic resource for understanding the evolutionary history, adaptive mechanisms, and biological characteristics of this species.</p>

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Chromosome-level genome assembly and annotation of the Triplophysa pappenheimi

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年11月21日

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  • Ying Li,
  • Dan Liu,
  • Zhanwen Yao,
  • Qiang Gao,
  • Cunfang Zhang,
  • Wei Wang,
  • Junmei Jia,
  • Sijia Liu,
  • Fei Tian,
  • Delin Qi

摘要

Triplophysa pappenheimi, an ecologically important species within the plateau freshwater ecosystem, predominantly inhabits the rapids of the upper Yellow River, its tributaries, and associated lakes, playing a crucial role in maintaining local aquatic biodiversity and serving as a model for plateau fish adaptation studies. In this study, we utilized a combination of Illumina short-read sequencing, PacBio HiFi long-read sequencing, and Hi-C technology to generate the first high-quality, chromosome-level genome assembly of T. pappenheimi. The assembled genome spans 626.33 Mb, organized into 25 pseudochromosomes, with a scaffold N50 of 24.41 Mb. We annotated 24,952 genes, representing 98.82% of the predicted protein-coding genes. In addition, we used GetOrganelle v1.7.7.1 to isolate and assemble the complete mitochondrial genome from the Illumina sequencing data, with a total length of 16,574 bp, and successfully achieved circularization. This high-quality genome assembly provides a valuable genomic resource for understanding the evolutionary history, adaptive mechanisms, and biological characteristics of this species.