Comparative analysis of the complete chloroplast genome of jack bean (Canavalia ensiformis, Fabaceae) revealed mutational hotspots and phylogenetic relationships

In recent years, the study of chloroplast genomes has gained increasing attention due to its significance in understanding plant evolution, phylogenetics, and genetic engineering. Canavalia ensiformis , commonly known as jack bean, is a leguminous plant of agricultural and ecological importance, with its chloroplast genome offering potential insights into adaptive mechanisms, species divergence, and biotechnological applications. This study focuses on the structure, organization, and gene content of the C. ensiformis chloroplast genome and its comparative analysis with other members of Phaseoleae (Fabaceae). We assembled and annotated the complete chloroplast genome of C. ensiformis using a combination of Illumina short-reads and Oxford Nanopore long-reads available on GenBank. The C. ensiformis chloroplast genome was organized as a single circular structure of 157,809 bp in length and divided into four main regions: a large single-copy (77,529 bp), a small single-copy (18,934 bp), and a pair of inverted repeat regions (30,673 bp). The genome encoded 95 protein-coding genes, 8 rRNA, and 37 tRNA genes. To explore evolutionary relationships, we conducted a comparative analysis of plastid genomes across Phaseoleae species. Structural variations, gene rearrangements, and divergence in non-coding regions were assessed, revealing conserved synteny and lineage-specific differences within the tribe. The phylogenomic analysis based on plastid genome sequences further clarified the evolutionary placement of C. ensiformis within Phaseoleae. The results contribute to a broader understanding of plastid genome evolution in legumes, one of the most species-rich plant families, and provide valuable genomic resources for future research in molecular phylogenetics and crop improvement.