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Background <p><i>Coreius guichenoti</i> is a critically endangered, nationally protected second-class endemic fish in the upper Yangtze River. Its wild population has declined sharply due to habitat degradation, overfishing, and dam construction, necessitating urgent conservation genomics resources.</p> Objective <p>To generate a high-quality chromosome-level genome assembly for <i>C. guichenoti</i> to elucidate its adaptive evolution and support conservation strategies.</p> Methods <p>We integrated PacBio HiFi long-read sequencing and Hi-C scaffolding technologies for de novo genome assembly. Genome annotation included repeat masking, protein-coding gene prediction, and functional characterization using public databases. Comparative genomics and phylogenetic analyses were performed with 13 related fish species.</p> Results <p>A 1.10&#xa0;Gb genome was assembled, with 93.56% of sequences anchored to 25 chromosomes (scaffold N50 = 41.37&#xa0;Mb). Repeat elements constituted 58.26% of the genome, and 25,588 protein-coding genes were predicted (96.1% functionally annotated). BUSCO completeness reached 99.7%. Phylogenetic analysis revealed that <i>C. guichenot</i>i diverged from <i>Leuciscus waleckii</i> ~ 79.8 million years ago. Synteny analysis showed significant chromosomal rearrangements between these species. Gene family expansions implicated immune adaptation (e.g., IL-17 signaling) and metabolic pathways (e.g., arachidonic acid metabolism).</p> Conclusion <p>This high-quality genome provides a critical resource for understanding adaptive evolution and guiding conservation strategies for this imperiled species.</p>

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High-quality chromosome-scale genome assembly and adaptive evolution analysis of Yangtze endemic Coreius guichenoti

  • 期刊论文

  • 发表日期：

    2026年1月23日

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  • Jing Chen,
  • Xianqi Peng,
  • Lei Huang,
  • Xialian Bu,
  • Yu Zhao,
  • Tao Qian,
  • Jian Zhu,
  • Huantao Qu,
  • Jiayun Yao

摘要

Background

Coreius guichenoti is a critically endangered, nationally protected second-class endemic fish in the upper Yangtze River. Its wild population has declined sharply due to habitat degradation, overfishing, and dam construction, necessitating urgent conservation genomics resources.

Objective

To generate a high-quality chromosome-level genome assembly for C. guichenoti to elucidate its adaptive evolution and support conservation strategies.

Methods

We integrated PacBio HiFi long-read sequencing and Hi-C scaffolding technologies for de novo genome assembly. Genome annotation included repeat masking, protein-coding gene prediction, and functional characterization using public databases. Comparative genomics and phylogenetic analyses were performed with 13 related fish species.

Results

A 1.10 Gb genome was assembled, with 93.56% of sequences anchored to 25 chromosomes (scaffold N50 = 41.37 Mb). Repeat elements constituted 58.26% of the genome, and 25,588 protein-coding genes were predicted (96.1% functionally annotated). BUSCO completeness reached 99.7%. Phylogenetic analysis revealed that C. guichenoti diverged from Leuciscus waleckii ~ 79.8 million years ago. Synteny analysis showed significant chromosomal rearrangements between these species. Gene family expansions implicated immune adaptation (e.g., IL-17 signaling) and metabolic pathways (e.g., arachidonic acid metabolism).

Conclusion

This high-quality genome provides a critical resource for understanding adaptive evolution and guiding conservation strategies for this imperiled species.