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

Authors: LEE, HYUNOH - Orise Fellow; WRIGHT, HALLIE - Hudsonalpha Institute For Biotechnology; Jordan, Brandon; BELAMKAR, VIKAS - Corteva Agriscience; SINGH, JUGPREET - University Of Florida; Kalberer, Scott; CLEVENGER, JOSH - Hudsonalpha Institute For Biotechnology; Cannon, Steven

Submitted to: Scientific Data
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/12/2026
Publication Date: 2/26/2026
Citation: Lee, H., Wright, H.C., Jordan, B.D., Belamkar, V., Singh, J., Kalberer, S.R., Clevenger, J., Cannon, S.B. 2026. Chromosome-level haplotype-resolved genome assemblies and annotations of Apios americana and Apios priceana. Scientific Data. 13. Article 544. https://doi.org/10.1038/s41597-026-06915-y.
DOI: https://doi.org/10.1038/s41597-026-06915-y

Interpretive Summary: Apios americana and Apios priceana are tuber-forming legumes native to North America with untapped agricultural potential. The data described in this manuscript includes the genome assemblies (the DNA sequences for all of the chromosomes) and the predicted genes (sequences, locations, and functional descriptions) for two edible North American species: Apios americana and Apios priceana. Apios americana, sometimes called "potato bean," produces starchy, high-protein tubers. The plant may be grown as a perennial crop. Apios americana is found throughout eastern and central North America, from Louisiana in the south to Quebec in the north. This species has traditionally been wild-harvested and used by indigenous peoples. Apios priceana, a relative of potato bean, is a rare legume species, found scattered locations in the North American Southeast (Alabama, Mississippi, Kentucky, and Tennessee). It has a vining habit and produces an edible, thickened storage root. The availability of these data sets will be helpful to researchers working to better understand and improve legume crops, and also potentially to improve the potato bean as a more productive perennial crop.

Technical Abstract: 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. In this study, we present high-quality, haplotype-resolved, chromosome-level genome assemblies for both species. For each genome, 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%, and over 25,000 protein-coding genes were predicted per haplotype. Repeat annotation revealed that over 80% of both genomes consist of interspersed repetitive elements, primarily long terminal repeat (LTR) retrotransposons. These genomic resources will support trait mapping and structural variation analyses in Apios, and more broadly, comparative genomics and gene family studies within Phaseoleae and the legume family. All data and annotations are freely accessible to support further research.