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<p><i>Spinibarbus caldwelli</i> is an economically important freshwater species within the Cyprinidae family, abundant in the middle and lower reaches of the Yangtze River and its adjacent basins. As a promising species suitable for aquaculture in southern China, the lack of genomic resources has hampered the genetic breeding and conservation. Here, we release a chromosome-level genome assembly for <i>S. caldwelli</i> using PacBio HiFi long-reads, Illumina short-reads, and Hi-C sequencing data. The final genome assembly is 1.77 Gb in size, with a contig N50 of 24.27 Mb. Using Hi-C scaffolding, 99.14% of the contigs were successfully anchored to 50 chromosomes, resulting in a scaffold N50 of 35.29 Mb. The final genome assembly shows a BUSCO completeness of 98.27%. The assembled genome contains 49.41% repetitive sequences and 51,505 predicted genes, 90.83% of which have been functionally annotated. This genome provides a genetic basis for <i>S. caldwelli</i>, facilitating the exploration of Cyprinid phylogeny, genetic improvement, and conservation efforts.</p>

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Chromosome-level genome assembly and annotation of Spinibarbus caldwelli

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年7月3日

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  • Ziyan Fan,
  • Wen Lei,
  • Yuan Fang,
  • Junqing Sheng,
  • Qingxiang Zeng,
  • Shaoqing Jian,
  • Lei Fang,
  • Yijiang Hong,
  • Wanchang Zhang

摘要

Spinibarbus caldwelli is an economically important freshwater species within the Cyprinidae family, abundant in the middle and lower reaches of the Yangtze River and its adjacent basins. As a promising species suitable for aquaculture in southern China, the lack of genomic resources has hampered the genetic breeding and conservation. Here, we release a chromosome-level genome assembly for S. caldwelli using PacBio HiFi long-reads, Illumina short-reads, and Hi-C sequencing data. The final genome assembly is 1.77 Gb in size, with a contig N50 of 24.27 Mb. Using Hi-C scaffolding, 99.14% of the contigs were successfully anchored to 50 chromosomes, resulting in a scaffold N50 of 35.29 Mb. The final genome assembly shows a BUSCO completeness of 98.27%. The assembled genome contains 49.41% repetitive sequences and 51,505 predicted genes, 90.83% of which have been functionally annotated. This genome provides a genetic basis for S. caldwelli, facilitating the exploration of Cyprinid phylogeny, genetic improvement, and conservation efforts.