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<p><i>Homatula variegata</i> is a small benthic loach from the upper Yangtze and adjacent basins with aquaculture and ornamental value but no reference genome. We present a near telomere-to-telomere (T2T) chromosome-level assembly built from PacBio HiFi, Oxford Nanopore ultra-long, Illumina short reads, and Hi-C. The 641.26-Mb genome resolves 24 chromosomes as single contigs (contig N50, 24.40 Mb). Hi-C confirms chromosome-length scaffolding; we detect 24 putative centromeres and 20 terminal telomeric tracts, with 22 chromosomes gap-free and two containing one gap. Annotation identifies 24,479 protein-coding genes, 93% functionally assigned, and 27.13% repetitive content dominated by DNA transposons. Quality assessments show high completeness (BUSCO, 96.48% complete) and base-level accuracy consistent with k-mer and read-mapping metrics. To our knowledge this is the first near T2T-level reference for any loach (Cobitoidei), filling a key gap in Cypriniformes genomics. This resource will enable comparative and population genomics, illuminate adaptation to montane stream habitats, and support selective breeding, conservation, and aquaculture of this native species.</p>

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A chromosome level genome assembly of Homatula variegata from the Yangtze River basin

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年1月26日

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  • Yong Tang,
  • Qiaoxing Wu,
  • Yusu Wang,
  • Shaoqi Jiang,
  • Lan Liu,
  • Lingjin Xian

摘要

Homatula variegata is a small benthic loach from the upper Yangtze and adjacent basins with aquaculture and ornamental value but no reference genome. We present a near telomere-to-telomere (T2T) chromosome-level assembly built from PacBio HiFi, Oxford Nanopore ultra-long, Illumina short reads, and Hi-C. The 641.26-Mb genome resolves 24 chromosomes as single contigs (contig N50, 24.40 Mb). Hi-C confirms chromosome-length scaffolding; we detect 24 putative centromeres and 20 terminal telomeric tracts, with 22 chromosomes gap-free and two containing one gap. Annotation identifies 24,479 protein-coding genes, 93% functionally assigned, and 27.13% repetitive content dominated by DNA transposons. Quality assessments show high completeness (BUSCO, 96.48% complete) and base-level accuracy consistent with k-mer and read-mapping metrics. To our knowledge this is the first near T2T-level reference for any loach (Cobitoidei), filling a key gap in Cypriniformes genomics. This resource will enable comparative and population genomics, illuminate adaptation to montane stream habitats, and support selective breeding, conservation, and aquaculture of this native species.