Chromosome-level haplotype-resolved genome assemblies and annotations of Apios americana and Apios priceana

Apios americana and Apios priceana are tuber-forming legumes native to North America with ecological value and agricultural potential. The lack of genomic resources has limited comparative studies and crop improvement for these species. Here, we report high-quality, haplotype-resolved, chromosome-level genome assemblies for both the species. The assemblies were generated from high-fidelity long-read data, and the primary assemblies were scaffolded using Omni-C chromatin conformation maps. The genome sizes of the primary haplotype assemblies were 1.53 Gb for A. americana and 1.85 Gb for A. priceana, each represented by 11 pseudochromosomes. The BUSCO completeness scores ranged from 98.6% to 99.0%. Approximately 26,000 predicted genes (30,000-33,000 predicted mRNA transcripts) were identified per haplotype in A. americana and A. priceana, respectively. Repeat annotation revealed that over 80% of both genomes consist of interspersed repetitive elements, with the most abundant being long terminal repeat (LTR) retrotransposons. These genomic resources will support trait mapping and structural variation analyses in Apios, and more broadly, comparative genomics within the legume family.