A chromosome-level genome assembly of the darkbarbel catfish Pelteobagrus vachelli

Abstract

The darkbarbel catfish (Pelteobagrus vachelli), an economically important aquaculture species in China, is extensively employed in hybrid yellow catfish production due to its superior growth rate. However, information on its genome has been limited, constraining further genetic studies and breeding programs. Leveraging the power of PacBio long-read sequencing and Hi-C technologies, we present a high-quality, chromosome-level genome assembly for the darkbarbel catfish. The resulting assembly spans 692.10 Mb, with an impressive 99.9% distribution over 26 chromosomes. The contig N50 and scaffold N50 are 13.30 Mb and 27.55 Mb, respectively. The genome is predicted to contain 22,109 protein-coding genes, with 96.1% having functional annotations. Repeat elements account for approximately 35.79% of the genomic landscape. The completeness of darkbarbel catfish genome assembly is highlighted by a BUSCO score of 99.07%. This high-quality genome assembly provides a critical resource for future hybrid catfish breeding, comparative genomics, and evolutionary studies in catfish and other related species.

Fig. 1

Overview of the genome assembly for darkbarbel catfish. (a) Flow chart illustrating the genome assembly pipeline for darkbarbel catfish. (b) Hi-C heatmap (200-kb resolution) showcasing the interaction frequencies between different chromosomes of darkbarbel catfish.

Fig. 2

Genomic landscape of darkbarbel catfish. Circos plot of darkbarbel catfish illustrating from outside to inside, gene density (a), GC content (b), and the densities of DNA transposons (c), LTRs (d), LINEs (e), and SINEs (f), all represented in 200-kb genomic windows.

Fig. 3

Venn diagram of function annotations from various databases. The Venn diagram displays the overlap and uniqueness of functional gene annotations derived from 4 databases: TrEMBL, NR, Siwss-Prot, and eggNOG.

Fig. 4

Chromosome sequence synteny comparisons. (a) Syntenic relationship between the darkbarbel catfish genome and the Chinese longsnout catfish genome. (b) Syntenic relationship between the darkbarbel catfish genome and the yellow catfish genome. Each line connects a pair of homologous sequences between the two species.