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<p><i>Cyprinus carpio</i> var. <i>Xiangxi</i> is a regionally farmed rice-field carp endemic to the Xiangxi region of Hunan Province, China. To adapt to the rice-fish farming environment, this variety has developed a range of genetic and physiological adaptations. However, genomic research on this strain remains limited. Here, we assembled a high-quality chromosome-level genome of <i>C. carpio</i> var. <i>Xiangxi</i> to fill this knowledge gap. Using PacBio HiFi, DNBSEQ, and Hi-C technology, We generated a 1.54 Gb genome with a contig N50 of 28.12 Mb. Using Hi-C data, 99.38% of the assembly (1,535.34 Mb) was anchored to 50 pseudochromosomes, yielding a scaffold N50 of 30.26 Mb. The quality value and Benchmarking Universal Single-Copy Ortholog score were 62.32 and 97.4%, respectively, indicating that our genome sequence is of high quality and completeness. A total of 46,362 protein-coding genes were predicted, of which 45,409 (97.94%) were functionally annotated. This study provides a valuable genomic resource for the conservation of <i>C. carpio</i> var. <i>Xiangxi</i> and offers new insights into the evolutionary history of common carp.</p>

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A high-quality chromosome-level genome assembly of the common carp (Cyprinus carpio var. Xiangxi)

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年10月13日

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  • Zhe Li,
  • Zi’ao Wang,
  • Yinghai Peng,
  • Yazhou Hu,
  • Xianwen Zhou

摘要

Cyprinus carpio var. Xiangxi is a regionally farmed rice-field carp endemic to the Xiangxi region of Hunan Province, China. To adapt to the rice-fish farming environment, this variety has developed a range of genetic and physiological adaptations. However, genomic research on this strain remains limited. Here, we assembled a high-quality chromosome-level genome of C. carpio var. Xiangxi to fill this knowledge gap. Using PacBio HiFi, DNBSEQ, and Hi-C technology, We generated a 1.54 Gb genome with a contig N50 of 28.12 Mb. Using Hi-C data, 99.38% of the assembly (1,535.34 Mb) was anchored to 50 pseudochromosomes, yielding a scaffold N50 of 30.26 Mb. The quality value and Benchmarking Universal Single-Copy Ortholog score were 62.32 and 97.4%, respectively, indicating that our genome sequence is of high quality and completeness. A total of 46,362 protein-coding genes were predicted, of which 45,409 (97.94%) were functionally annotated. This study provides a valuable genomic resource for the conservation of C. carpio var. Xiangxi and offers new insights into the evolutionary history of common carp.