Comparative Plastid Phylogenomics of 29 Newly Sequenced Bougainvillea Cultivars Resolves the Phylogenetic Placement of Double-Bracted Cultivars

Bougainvillea (Nyctaginaceae) cultivars are horticulturally prized worldwide for their vivid bracts; however, repeated interspecific hybridization and somatic mutations have obscured their maternal origins, particularly for double-bracted forms. Here, we sequenced and assembled the complete plastomes of 29 cultivars (16 double-bracted, 13 single-bracted) and conducted comparative and phylogenomic analyses alongside 15 published taxa. All plastomes displayed a conserved quadripartite structure (153,994–154,542 bp, comprising 130–131 functional genes), with B. × buttiana ‘Mahara Variegated’ harboring a pseudogenized ycf1 caused by a verified frameshift-induced premature stop codon, serving as a unique diagnostic marker for this cultivar. Sequence divergence was largely confined to intergenic spacers, identifying trnH-GUG–psbA and trnS-GCU–trnG-UCC as potential DNA barcodes for species-level discrimination. Conversely, intraspecific variation was virtually absent; 13 double-bracted accessions were completely sequence-identical. Phylogenomic analyses resolved interspecific backbones (B. spectabilis, B. peruviana, and B. glabra) well but placed nearly all double-bracted cultivars into an unresolved polytomy alongside single-bracted B. × buttiana lineages (including ‘Mrs. Butt’). This confirms a shared maternal origin and demonstrates that double-bracted phenotypes predominantly arose through recurrent somatic bud mutations rather than independent hybridizations. Furthermore, identical plastomes across distinct phenotypes highlight the inherent resolution limits of maternal markers for cultivar delimitation. Overall, our study enriches Bougainvillea genomic resources, clarifies previously ambiguous maternal lineages among cultivated taxa, and demonstrates that cultivar-level discrimination must rely on nuclear rather than plastid genomic markers.