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<p>Red crucian carp, a variant of <i>Carassius auratus</i>, has a long history of cultivation as both a food and an ornamental fish. Here, we integrated MGI short-reads, PacBio HiFi long-reads, ONT ultra-long reads, and Hi-C sequencing data to assemble a nearly telomere-to-telomere (T2T) genome for this species, containing only four gaps. This assembly, which consists of a primary haplotype containing 50 chromosomes, covers 99.88% of the sequence, with a total length of 1.55 Gb, and reveals 93 telomeres and 50 centromeres. Key quality metrics for the assembly include a contig N50 of 29.92 Mb (contiguity), a BUSCO score of 99.40% (completeness), and a consensus quality value of 64.44 (correctness), collectively reflecting a high-quality genome. Annotation identified 46,061 protein-coding genes and 679.10 Mb (43.72% of the assembly) of repetitive sequences. Furthermore, 22,454 tRNAs, 42,628 rRNAs, 3,309 miRNAs, and 3,380 snRNAs were annotated. This represents the first near-T2T genome assembly for any species within the genus <i>Carassius</i>, offering a valuable genomic resource for investigating the biological traits of the red crucian carp and advancing research in evolutionary genomics.</p>

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A near telomere to telomere genome assembly of red crucian carp (Carassius auratus red var.)

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月28日

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  • Zhengkun Liu,
  • Chongqing Wang,
  • Kun Zhang,
  • Yuhan Yang,
  • Zeyang Li,
  • Qian Xiao,
  • Xu Huang,
  • Xiaowei Xu,
  • Xidan Xu,
  • Yue Zhou,
  • Jinhai Bai,
  • Yuchen Jiang,
  • Wanjing Peng,
  • Ling Xiong,
  • Enkui Hu,
  • Siyang Li,
  • Qinbo Qin

摘要

Red crucian carp, a variant of Carassius auratus, has a long history of cultivation as both a food and an ornamental fish. Here, we integrated MGI short-reads, PacBio HiFi long-reads, ONT ultra-long reads, and Hi-C sequencing data to assemble a nearly telomere-to-telomere (T2T) genome for this species, containing only four gaps. This assembly, which consists of a primary haplotype containing 50 chromosomes, covers 99.88% of the sequence, with a total length of 1.55 Gb, and reveals 93 telomeres and 50 centromeres. Key quality metrics for the assembly include a contig N50 of 29.92 Mb (contiguity), a BUSCO score of 99.40% (completeness), and a consensus quality value of 64.44 (correctness), collectively reflecting a high-quality genome. Annotation identified 46,061 protein-coding genes and 679.10 Mb (43.72% of the assembly) of repetitive sequences. Furthermore, 22,454 tRNAs, 42,628 rRNAs, 3,309 miRNAs, and 3,380 snRNAs were annotated. This represents the first near-T2T genome assembly for any species within the genus Carassius, offering a valuable genomic resource for investigating the biological traits of the red crucian carp and advancing research in evolutionary genomics.