Abstract: The generic delimitation of the Caesalpinia group continues to be under contention, similar to several other lineages of the hyper diverse legume family. Despite its known ecological and economic importance and role as a model to explore correlations between ecological diversification and genomic traits, both intergeneric and infrageneric relationships remain unresolved, despite recent phylogenetic analyses. While phylogenomic approaches have elucidated complex relationships within the angiosperm tree of life, the phylogenetic backbone of the Caesalpinia group remains poorly defined owing to limited genomic data. To address this gap, this study combined de novo assembled and characterized plastomes from 19 samples across nine genera, along with 27 previously published plastomes, to achieve a comprehensive dataset of 46 plastomes representing 16 of the 26 genera. The phylogenomic analysis generated a robust phylogenetic hypothesis, distinguishing two main clades, of which one occurs exclusively in the Neotropics in contrast to the other Pantropical clade, in addition to resolving several previously ambiguous relationships. Notable changes in the plastome gene content were observed, including six gene losses (psbL, rpl22, rps2, rpl32, ycf1, ycf2) and six gene duplications (ndhB, rpl23, rps7, rps12, ycf1, ycf2). Other changes included shifts in inverted repeat (IR) boundaries and genome rearrangements, indicating lineage-specific plastome evolution. Hypervariable regions were identified as potential mini-barcodes, with cpSSRs providing valuable resources for species delimitation and population genetics studies. Codon usage revealed a strong AT bias, while relaxed purifying selection in genes such as accD, clpP, and rps16. These findings offer novel insights into Caesalpinia group evolution, emphasizing the utility of plastome data for resolving complex evolutionary questions and establishing a genomic toolkit for future research in systematics, conservation, and evolutionary biology of legumes.

Key words: phylogenomics, gene evolution, gene duplications, gene loss, genomic rearrangements, generic flux, ecological adaptation, conservation genomics, species delimitation.