Background: Clematisspecies are attractive ornamental plants with a variety of flower colors and patterns. Heat stress is one of the main factors restricting the growth, development, and ornamental value ofClematis.Clematis lanuginosaandClematis crassifoliaare large-flowered and evergreenClematisspecies, respectively, that show different tolerance to heat stress. We compared and analyzed the transcriptome ofC. lanuginoseandC. crassifoliaunder heat stress to determine the regulatory mechanism(s) of resistance.Results: A total of 1720 and 6178 differentially expressed genes were identified fromC. lanuginoseandC. crassifolia, respectively. The photosynthesis and oxidation–reduction processes ofC. crassifoliawere more sensitive thanC. lanuginoseunder heat stress. Glycine/serine/threonine metabolism, glyoxylic metabolism, and thiamine metabolism were important pathways in response to heat stress inC. lanuginose, and flavonoid biosynthesis, phenylalanine metabolism, and arginine/proline metabolism were the key pathways inC. crassifolia. SixsHSPs (c176964_g1, c200771_g1, c204924_g1, c199407_g2, c201522_g2, c192936_g1),POD1(c200317_g1),POD3(c210145_g2),DREB2(c182557_g1), andHSFA2(c206233_g2) may be key genes in the response to heat stress inC. lanuginoseandC. crassifolia.Conclusions: We compared important metabolic pathways and differentially expressed genes in response to heat stress betweenC. lanuginoseandC. crassifolia. The results increase our understanding of the response mechanism and candidate genes ofClematisunder heat stress. These data may contribute to the development of newClematisvarieties with greater heat tolerance.

Bougainvillea, an increasingly popular ornamental plant known for its vibrant colours and extended flowering period. Due to the complexities of classification systems and the serious phenomenon of homonym in Bougainvillea, this study utilized simplified genome sequencing technology (ddRAD) to explore the genetic background of 84 Bougainvillea varieties.756,078 SNPs were utilized to analyse the genetic diversity, genetic structure, and genetic relationships among these cultivars. The results indicated that all samples were categorized into six subpopulations (B1, B2, B3, B4, B5, B6), with low genetic diversity observed in all subpopulations except B5. Notably, there was significant gene flow and infiltration among different subpopulations, and most varieties exhibited no apparent kinship to one another. Additionally, selective sweep analysis identified 38 commonly selected sites across the six Bougainvillea subpopulations. These sites are primarily enriched in biosynthesis pathways related to sesquiterpenoids and triterpenoids, as well as glycerophospholipid metabolism, which may be associated with the directional artificial domestication of Bougainvillea and its susceptibility to bud mutation. This study not only uncovered the complex genetic background of Bougainvillea but also emphasized the considerable genetic differentiation within the subpopulations, thereby providing a foundation for future association studies and targeted breeding efforts.