Chromosome-level genome assembly of the cyprinid fish Onychostoma lini using PacBio HiFi and Hi-C sequencing
TL;DR
This high-quality reference genome provides a foundational resource for investigating cyprinid evolution, environmental adaptation, and molecular breeding, and supports the conservation of O. lini.
Abstract
Onychostoma lini is an ecologically and economically important cyprinid species endemic to the mountain rivers of southern China. Wild populations have sharply declined due to habitat fragmentation, hydropower development, and overexploitation, yet genomic information remains unavailable, hindering studies on its diversity, adaptation, and conservation. Here, we assembled the first chromosome-level genome of O. lini using PacBio HiFi long-read sequencing, Illumina short-read polishing, and Hi-C scaffolding. The 907.5 Mb assembly achieved a contig N50 of 32.83 Mb and a scaffold N50 of 34.89 Mb, with 99.93% of sequences anchored to 25 chromosomes. Repetitive elements occupied 387.36 Mb, representing 42.69% of the genome. We predicted 28,597 protein-coding genes, 99.05% of which were functionally annotated in NR, KEGG, InterPro, SwissProt, and GO databases. BUSCO analysis identified 97.9% complete orthologs, confirming assembly completeness and annotation accuracy. This high-quality reference genome provides a foundational resource for investigating cyprinid evolution, environmental adaptation, and molecular breeding, and supports the conservation of O. lini .