Chloroplast DNA barcoding of Cananga odorata using rbcL and trnL-F markers reveals intraspecific genetic structures

Cananga odorata (Lam.) Hook. f. & Thomson, valued for its aromatic flowers and horticultural use, displays extensive morphological and biochemical variation across Southeast Asia. Despite its economic importance, the intraspecific genetic structure of C. odorata remains poorly resolved. To assess genetic divergence, we analyzed 23 cultivated accessions using chloroplast DNA barcoding with the rbcL gene and trnL-F intergenic spacer. Sequence alignments, transition/transversion ratios, and phylogenetic reconstruction with maximum likelihood were performed on individual and concatenated datasets. Overall sequence identity was ≥ 98%, but multiple parsimony-informative sites were detected, especially in the noncoding trnL-F region, which showed higher variability than rbcL. Phylogenetic analyses consistently resolved three tentative clusterings. One lineage, corresponding to C. odorata forma genuina, was genetically distinct from other accessions. This divergence was defined by unique substitutions, including rbcL sites 329 (G → A) and 349 (A → G), and trnL-F sites 173 (A → C), 191 (C → A), and 506 (A → G). These markers represent the first molecular evidence linking chloroplast variants with forma-level differentiation in C. odorata. Our findings highlight the utility of plastid barcodes in resolving intraspecific structure and support their application in varietal identification, taxonomic refinement, and conservation strategies. Expanding analyses to nuclear genomic markers and broader geographic sampling will further elucidate lineage divergence, domestication history, and germplasm diversity in C. odorata.