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<p>Stone flounder (<i>Kareius bicoloratus</i>) is an emerging commercially important flatfish species in China, Japan, Korea, and Taiwan, because of its significant industrial value. However, no stone flounder genome sequence was reported to date, which greatly hinders the research on genetics and evolutionary genomics. In this study, we successfully assembled the first gap-free telomere-to-telomere (T2T) genome of stone flounder combining Illumina short-reads sequencing, PacBio HiFi sequencing, Hi-C sequencing, and ONT ultra-long sequencing. The genome spans 587.80 Mb with a contig N50 of 25.64 Mb. 98.58% of the genome sequences were assembled onto 24 chromosomes without gaps. Telomeres were identified at both ends of 8 chromosomes and at one end of 15 chromosomes. We identified 128.10 Mb repetitive sequences and 22,312 protein-coding genes, among which 98.03% of the coding genes were functionally annotated. BUSCO assessment, mapping ratio, and quality value (QV) evaluation collectively indicated the high quality and completeness of the genome assembly. This work advances the progress of evolutionary genomics, genetics and molecular genetic breeding research on stone flounder.</p>

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Gap-free telomere-to-telomere genome assembly of stone flounder (Kareius bicoloratus)

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年6月22日

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  • Weiwei Zheng,
  • Kaiqiang Liu,
  • Tao Yang,
  • Dong Xu,
  • Zhihong Liu,
  • Wei Yuan,
  • Yan Liu,
  • Tengteng Wang,
  • Huizong Han,
  • Xueyan Fang,
  • Wenteng Xu,
  • Songlin Chen

摘要

Stone flounder (Kareius bicoloratus) is an emerging commercially important flatfish species in China, Japan, Korea, and Taiwan, because of its significant industrial value. However, no stone flounder genome sequence was reported to date, which greatly hinders the research on genetics and evolutionary genomics. In this study, we successfully assembled the first gap-free telomere-to-telomere (T2T) genome of stone flounder combining Illumina short-reads sequencing, PacBio HiFi sequencing, Hi-C sequencing, and ONT ultra-long sequencing. The genome spans 587.80 Mb with a contig N50 of 25.64 Mb. 98.58% of the genome sequences were assembled onto 24 chromosomes without gaps. Telomeres were identified at both ends of 8 chromosomes and at one end of 15 chromosomes. We identified 128.10 Mb repetitive sequences and 22,312 protein-coding genes, among which 98.03% of the coding genes were functionally annotated. BUSCO assessment, mapping ratio, and quality value (QV) evaluation collectively indicated the high quality and completeness of the genome assembly. This work advances the progress of evolutionary genomics, genetics and molecular genetic breeding research on stone flounder.