Bougainvillea is popular in ornamental horticulture for its colorful bracts and excellent adaptability, but the complex genetic relationship among this genus is fuzzy due to limited genomic data. To reveal more genomic resources of Bougainvillea, we sequenced and assembled the complete chloroplast (cp) genome sequences of Bougainvillea spectabilis ‘Splendens’. The cp genome size was 154,869 bp in length, containing 86 protein-coding genes, 38 tRNAs, and eight rRNAs. Cp genome comparison across 12 Bougainvillea species (B. spectabilis, B. glabra, B. peruviana, B. arborea, B. praecox, B. stipitata, B. campanulata, B. berberidifolia, B. infesta, B. modesta, B. spinosa, and B. pachyphylla) revealed five mutational hotspots. Phylogenetic analysis suggested that B. spectabilis published previously and B. glabra clustered into one subclade as two distinct groups, sister to the subclade of B. spectabilis ‘Splendens’. We considered the phylogeny relationships between B. spectabilis and B. glabra to be controversial. Based on two hypervariable regions and three common plastid regions, we developed five molecular markers for species identification in Bougainvillea and applied them to classify 53 ornamental Bougainvillea cultivars. This study provides a valuable genetic resource for Bougainvillea breeding and offers effective molecular markers to distinguish the representative ornamental species of Bougainvillea.

Bougainvillea spp. is a well-known ornamental plant that is widely applied in urban landscaping construction. The colorful bracts of Bougainvillea in full bloom become important for urban landscape during special festivals. Although flowering regulation measures of Bougainvillea attracted much attention, the underlying mechanism of flower bud differentiation and development remains poorly understood. Here, we induced flowering of Bougainvillea glabra ‘Sao Paulo’ under 6-BA treatment and conducted RNA sequencing data analysis to characterize the molecular regulatory mechanism of flower development in response to 6-BA. Transcriptome analysis indicated that a series of genes and transcription factors of cytokinin metabolism, flowering and floral development regulation, and photoperiod regulation were upregulated by the 6-BA treatment, including COL, AP2, FT, SOC1, LFY, SPL4, SPL9, and SPL13. Moreover, the expression of these important genes exhibited relatively high levels of thorns compared to apical buds, suggesting that flower bud differentiation probably starts with the thorns in Bougainvillea. This study confirms that 6-BA treatment at certain concentrations can promote flowering of Bougainvillea and provides insight into the regulatory mechanism of the growth regulator acting on early flowering of Bougainvillea.

The two-component system (TCS) regulates key processes in plant growth, development, and stress response. Although TCS genes have been studied in model plants such as Arabidopsis and tomato, in petunia ( Petunia axillaris ), a model ornamental species, they remain poorly characterized at the genome-wide level. This study aimed to perform a comprehensive genome-wide analysis of TCS genes in petunia and investigate their expression patterns in response to hormones and abiotic stresses. A total of 74 TCS genes were identified, comprising 24 histidine kinases/histidine kinase-like (HK(L)s), 10 histidine phosphotransfers (HPs), and 40 response regulators (RRs). Comprehensive analyses of gene structures, conserved domains, and phylogenetic relationships suggested potential evolutionary divergence and functional specialization within TCS gene families. Tissue-specific expression profiles obtained via qRT-PCR revealed higher expression of TCS genes in leaves and roots. Analysis of cis -regulatory elements (CREs) indicated an enrichment of hormone- and stress-responsive motifs in petunia TCS promoters, with the abscisic acid (ABA)-responsive element (ABRE) being the most abundant, found in 63 genes, followed by the anaerobic response (ARE) and stress response (STRE) elements. We further analyzed response patterns to exogenous hormones (trans-zeatin (tZ) and ABA) and abiotic stresses (drought and salinity) using qRT-PCR. Compared to untreated controls, many TCS genes exhibited statistically significant up- and down-regulation (|log2FC| > 1, p < 0.05). These findings provide new insights into the regulatory roles of TCS genes in Petunia and identify candidate regulators for functional validation and molecular breeding to improve the floral traits and stress tolerance of ornamental plants.