Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4)

Common bean is a significant grain legume in human diets. However, the lack of a complete reference genome for common beans has hindered efforts to improve agronomic cultivars.

Herein, we present the first telomere-to-telomere (T2T) genome assembly of common bean (Phaseolus vulgaris L., YP4) using PacBio High-Fidelity reads, ONT ultra-long sequencing, and Hi-C technologies. The assembly resulted in a genome size of 560.30 Mb with an N50 of 55.11 Mb, exhibiting high completeness and accuracy (BUSCO score: 99.5%, quality value (QV): 54.86). The sequences were anchored into 11 chromosomes, with 20 of 22 telomeres identified, leading to the formation of 9 T2T pseudomolecules. Furthermore, we identified repetitive elements accounting for 61.20% of the genome and predicted 29,925 protein-coding genes. Phylogenetic analysis suggested an estimated divergence time of approximately 11.6 million years ago between P. vulgaris and Vigna angularis. Comparative genome analysis revealed the expanded gene families and variations between YP4 and G19833 associated with defense response.

The T2T reference genome and genomic insights presented here are crucial for future genetic studies not only in common bean but also in other legumes.