Chromosome-level assembly and annotation of the yellow-shelled fish (Barbodes Wynaadensis).

Barbodes wynaadensis, a unique cyprinid species native to Yunnan Province in China, stands out as an allotetraploid (AABB) fish with a complex evolutionary history. Leveraging a multi-platform sequencing strategy combining MGI short-read, PacBio long-read, and Hi-C scaffolding technologies, we assembled the first chromosome-level genome for B. wynaadensis. The final assembled genome spans 1.76 Gb in length with a contig N50 of 33.53 Mb, demonstrating high assembly continuity. Hi-C scaffolding enabled the reconstruction of 50 pseudochromosomes, representing 99.94% of the total genome assembly. Genome annotation identified 46,121 protein-coding genes, with a functional annotation rate of 99.76%. Repetitive elements constituted 48.26% of the genomic sequences, including lineage-specific expansions of DNA transposons (29.26%) and LTRs (6.36%). This high-quality assembly resolves challenges in polyploid genome reconstruction and provides a critical resource for investigating Cyprinidae evolution, particularly subgenome divergence and adaptation. The dataset also enables practical applications, such as molecular marker development for population monitoring, supporting conservation efforts for this threatened endemic species amid habitat degradation in the Nujiang River basin.