Aquaculture species such as tambaqui (Colossoma macropomum) and pacu (Piaractus mesopotamicus) are economically important freshwater fishes in South America. High-quality reference genomes greatly facilitate the discovery of genetic markers and functional elements, enabling selective breeding and improving sustainability in aquaculture. However, no chromosome-level, haplotype-resolved genome assemblies were previously available for these species. In this work, we aimed to generate chromosome-scale, haplotype-resolved genome assemblies for pacu and tambaqui using a trio binning approach.
We sequenced a hybrid offspring , named “tambacu”, obtained by crossing a male pacu and a female tambaqui. PacBio HiFi reads from the hybrid were partitioned by parental k-mers using YAK, assigning each read to either the pacu (paternal) or tambaqui (maternal) haplotype. Each haplotype was assembled de novo with HIFIASM, and redundant haplotigs were removed. The draft contig assemblies were evaluated for continuity (Table 1) and completeness.
Both assemblies are highly complete, with >98% of single-copy BUSCO genes. Hi-C scaffolding anchored the contigs into 27 chromosome-length scaffolds for pacu (Fig. 1A) and tambaqui (Fig 1B) , matching the known diploid karyotype (2n = 54) of these fishes. The Hi-C contact maps (Figure 1) show clear interaction matrices with 27 major diagonal blocks.
We also identified telomeric repeats (TTAGGG) at the ends of most chromosome scaffolds, supporting the structural accuracy of the assemblies. We predicted 40,814 protein-coding genes in the pacu assembly and 44,619 in the tambaqui assembly, along with tens of thousands of mRNAs, exons, and introns. These genomic resources are expected to support the development of more efficient and sustainable aquaculture for pacu and tambaqui.