The common bean (Phaseolus vulgaris L.) is an economically important food crop grown worldwide; however, its production is affected by various environmental stresses, including cold, heat, and drought stress. The plant U-box (PUB) protein family participates in various biological processes and stress responses, but the gene function and expression patterns of its members in the common bean remain unclear. Here, we systematically identified 63 U-box genes, including 8 tandem genes and 55 non-tandem genes, in the common bean. These PvPUB genes were unevenly distributed across 11 chromosomes, with chromosome 2 holding the most members of the PUB family, containing 10 PUB genes. The analysis of the phylogenetic tree classified the 63 PUB genes into three groups. Moreover, transcriptome analysis based on cold-tolerant and cold-sensitive varieties identified 4 differentially expressed PvPUB genes, suggesting their roles in cold tolerance. Taken together, this study serves as a valuable resource for exploring the functional aspects of the common bean U-box gene family and offers crucial theoretical support for the development of new cold-tolerant common bean varieties.

Common bean (Phaseolus vulgaris L.) is an economically important grain legume for the human diet and sustainable agricultural development. Snap bean, a vegetable-type common bean cultivated for edible immature pods, serves as a crucial dietary source of essential vitamins, minerals and proteins. However, its evolutionary and domestication history remains poorly characterized. Here, we assembled and characterized the complete chloroplast genome of snap bean using PacBio HiFi sequencing technology. The chloroplast genome formed a single circular molecule of 150,248 bp, consisting of a pair of inverted repeat regions, a large single-copy region, and a small single-copy region. A total of 75 protein-coding genes, 37 tRNA genes, and 8 rRNA genes were annotated. Phylogenomics revealed that snap bean has the closest relationship with dry common bean, grouping with lima bean; Phaseolus is phylogenetically nearest to Vigna. Comparative plastid genomics identified variants in accD, rpoC2, matK, and other coding genes. Nucleotide diversity analysis detected several highly variable hotspot regions, including accD, trnY-psbD, ndhH, and ycf1-rps15, which are promising informative plastid markers for phylogeny and population genetics. These findings deepen our understanding of legume chloroplast evolution and lay genomic foundations for common bean phylogenetic research and genetic breeding improvement.