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<p><i>Triplophysa erythraea</i>, a distinctive blind cave fish endemic to Hunan’s karst caves, faces significant threats due to its restricted range and fragile habitat. The high-quality genome assembly offers essential data for developing conservation strategies, and could be helpful to reveal adaptive mechanisms along with functional drivers behind <i>T. erythraea</i>’s unique morphological traits. In this study, we successfully assembled the telomere-to-telomere (T2T) genome of <i>T. erythraea</i>. The genome size was 757.23 Mb, with a contig N50 size of 27.63 Mb and a scaffold N50 size of 29.01 Mb. The Hi-C assembly placed 97.5% of the sequences onto 25 pseudo-chromosomes. Remarkably, 19 chromosomes were assembled into contiguous, gap-free scaffolds. Furthermore, 378.05 Mb (49.93%) of repetitive sequences and 25,179 protein-coding genes were identified, and 99.09% of the protein-coding genes were annotated. Comparative genomic analysis confirmed the genome’s high completeness, continuity, and accuracy. The genomic quality was further substantiated by a QV of 51.03 and a 98.38% of BUSCO completeness rate, assessed against the <i>T. erythraea</i> T2T genome assembly. This study serves as a key genetic resource for Nemacheilidae hypogean fishes and will be highly valuable for delineating adaptive genetic mechanisms of cave-adapted <i>Triplophysa</i> stone loaches.</p>

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The telomere-to-telomere genome assembly of the Triplophysa erythraea (Nemacheilidae hypogean fishes)

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月10日

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  • Chongrui Wang,
  • Xin Yang,
  • Dong Liu,
  • Wenwen Suo,
  • Hong Li,
  • Jinhui Pu,
  • Xiangrong Liu,
  • Qianqian Ku,
  • Xiping Yuan,
  • Yuejuan Zhou,
  • Qianhong Gu,
  • Dongsheng Ou

摘要

Triplophysa erythraea, a distinctive blind cave fish endemic to Hunan’s karst caves, faces significant threats due to its restricted range and fragile habitat. The high-quality genome assembly offers essential data for developing conservation strategies, and could be helpful to reveal adaptive mechanisms along with functional drivers behind T. erythraea’s unique morphological traits. In this study, we successfully assembled the telomere-to-telomere (T2T) genome of T. erythraea. The genome size was 757.23 Mb, with a contig N50 size of 27.63 Mb and a scaffold N50 size of 29.01 Mb. The Hi-C assembly placed 97.5% of the sequences onto 25 pseudo-chromosomes. Remarkably, 19 chromosomes were assembled into contiguous, gap-free scaffolds. Furthermore, 378.05 Mb (49.93%) of repetitive sequences and 25,179 protein-coding genes were identified, and 99.09% of the protein-coding genes were annotated. Comparative genomic analysis confirmed the genome’s high completeness, continuity, and accuracy. The genomic quality was further substantiated by a QV of 51.03 and a 98.38% of BUSCO completeness rate, assessed against the T. erythraea T2T genome assembly. This study serves as a key genetic resource for Nemacheilidae hypogean fishes and will be highly valuable for delineating adaptive genetic mechanisms of cave-adapted Triplophysa stone loaches.