Chromosome-level genome assembly of a critically endangered species Leuciscus chuanchicus

TL;DR

Researchers assembled a high-quality genome for the critically endangered fish Leuciscus chuanchicus, providing a valuable resource for conservation and evolutionary studies.

Contribution

The study provides the first chromosome-level genome assembly for Leuciscus chuanchicus using a combination of Illumina, PacBio HiFi, and Hi-C data.

Findings

The assembled genome has a size of 1.16 Gb with high contiguity (contig N50 of 31.1 million bp and scaffold N50 of 43.9 million bp).

The genome includes 31,196 predicted protein-coding genes, with 90.79% functionally annotated.

The genome assembly achieved high completeness with 97.6% completeness according to BUSCO and 91.28% according to OMArk.

Abstract

Leuciscus chuanchicus, a critically endangered cyprinid endemic in the Yellow River, represents an evolutionary significant lineage within Leuciscinae. However, conservation efforts for this species have been hindered by the lack of genetic and genomic resources. Here we reported a high-quality chromosome-level genome of L. chuanchicus by combining Illumina reads, PacBio HiFi long reads and Hi-C data. The assembled genome size was 1.16 Gb, with a contig N50 size of 31,116,631 bp and a scaffold N50 size of 43,855,677 bp. The resulting 130 scaffolds were further clustered and ordered into 25 chromosomes based on the Hi-C data, representing 97.84% of the assembled sequences. The genome contained 60.36% repetitive sequences and 35,014 noncoding RNAs. A total of 31,196 protein-coding genes were predicted, of which 28,323 (90.79%) were functionally annotated. The BUSCO and OMArk revealed 97.6% and 91.28% completion rates, respectively. This study assembled a high-quality genome of L. chuanchicus, and provided fundamental genomic resources for investigating the molecular mechanism and evolution of the Leuciscinae.

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