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<p><i>Troglonectes daqikongensis</i> is an obligate cave-dwelling fish with a narrowly restricted distribution in southwestern China and pronounced troglomorphic traits. Despite its ecological and evolutionary significance, genomic resources for this species remain scarce. Here, we report a chromosome-level reference genome of <i>Troglonectes daqikongensis</i>, assembled using PacBio HiFi long reads, Hi-C data, and MGI T7 short reads. The final assembly spans 615.17 Mb across 47 scaffolds, with a contig N50 of 20.92 Mb and a scaffold N50 of 23.57 Mb. In total, 97.96% of the assembly was anchored to 25 pseudo-chromosomes. Repetitive elements comprise 276.51 Mb, accounting for 44.95% of the genome. A total of 24,652 protein-coding genes were predicted using a combination of <i>de novo</i> prediction, homology-based annotation, and transcriptome evidence, with 99.89% functionally annotated. BUSCO assessments indicated high completeness for both the genome assembly (96.6%) and gene annotation (95.5%). This high-quality genome provides a foundational resource for evolutionary and ecological research, including studies on the genetic basis of cave adaptation and the conservation of the microendemic species <i>Troglonectes daqikongensis</i>.</p>

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Chromosome-level genome assembly of the obligate cave loach Troglonectes daqikongensis

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月5日

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  • Houhua Bing,
  • Wenyu Fang,
  • Jiayang He,
  • Yongrui Lu,
  • Zichen Xiong,
  • Jun Xu,
  • Guohuan Su

摘要

Troglonectes daqikongensis is an obligate cave-dwelling fish with a narrowly restricted distribution in southwestern China and pronounced troglomorphic traits. Despite its ecological and evolutionary significance, genomic resources for this species remain scarce. Here, we report a chromosome-level reference genome of Troglonectes daqikongensis, assembled using PacBio HiFi long reads, Hi-C data, and MGI T7 short reads. The final assembly spans 615.17 Mb across 47 scaffolds, with a contig N50 of 20.92 Mb and a scaffold N50 of 23.57 Mb. In total, 97.96% of the assembly was anchored to 25 pseudo-chromosomes. Repetitive elements comprise 276.51 Mb, accounting for 44.95% of the genome. A total of 24,652 protein-coding genes were predicted using a combination of de novo prediction, homology-based annotation, and transcriptome evidence, with 99.89% functionally annotated. BUSCO assessments indicated high completeness for both the genome assembly (96.6%) and gene annotation (95.5%). This high-quality genome provides a foundational resource for evolutionary and ecological research, including studies on the genetic basis of cave adaptation and the conservation of the microendemic species Troglonectes daqikongensis.