Background: Curcubita ficifolia Bouché (Cucurbitaceae) has high value as a food crop and medicinal plant, and also has horticultural value as rootstock for other melon species. China is home to many different cultivars, but the genetic diversity of these resources and the evolutionary relationships among them, as well as the differences between C. ficifolia and other Cucurbita species, remain unclear. Results: We investigated the chloroplast (cp) genomes of 160 C. ficifolia individuals from 31 populations in Yunnan, a major C. ficifolia production area in China. We found that the cp genome of C. ficifolia is ~151 kb and contains 128 genes, of which 86 are protein coding genes, 34 encode tRNA, and eight encode rRNAs. We also identified 64 SSRs, mainly AT repeats. The cp genome was found to contain a total of 204 SNP and 57 indels, and a total of 21 haplotypes were found in the 160 study individuals. The reverse repeat (IR) region of C. ficifolia contained a few differences compared with this region in the six other Cucurbita species. Sequence difference analysis demonstrated that most of the variable regions were concentrated in the single copy (SC) region. Moreover, the sequences of the coding regions were found to be more similar among species than those of the non-coding regions. The phylogenies reconstructed from the cp genomes of 61 representative species of Cucurbitaceae reflected the currently accepted classification, in which C. ficifolia is sister to the other Cucurbita species, however, different interspecific relationships were found between Cucurbita species. Conclusions: These results will be valuable in the classification of C. ficifolia genetic resources and will contribute to our understanding of evolutionary relationships within the genus Cucurbita.

Background: Dendrobium devonianum is a traditional Chinese medicinal herb with notable ornamental and medicinal value. Methods: In this study, transcriptomic and metabolomic approaches were employed to investigate gene expression and secondary metabolite changes during four developmental stages of D. devonianum flowers. Results: Metabolomic analysis identified 1186 distinct metabolites, with flavonoid compounds being the most abundant category (213 types). Transcriptomic analysis revealed 31 differentially expressed genes associated with flavonoid biosynthesis and flavonoid and flavonol biosynthesis pathways. Among these, key genes regulating flavonol synthesis, including F3H (Unigene0077194) and FLS (Unigene0062137), exhibited high expression levels in the early developmental stage (S1). Conclusions: Flavonoids serve as the major active components in D. devonianum flowers, exhibiting a wide range of pharmacological properties. This study provides valuable insights into the molecular mechanisms driving flavonoid accumulation in D. devonianum, offering a foundation for further functional studies and applications in ornamental and medicinal plant research.

Dendrobium devonianum is an important medicinal plant, rich in flavonoid, with various pharmacological activities such as stomachic and antioxidant properties. In this study, we integrated metabolome and transcriptome analyses to reveal metabolite and gene expression profiles of D. devonianum, both green (GDd) and purple-red (RDd) of semi-annual and annual stems. A total of 244 flavonoid metabolites, mainly flavones and flavonols, were identified and annotated. Cyanidin and delphinidin were the major anthocyanidins, with cyanidin-3-O-(6″-O-p-Coumaroyl) glucoside and delphinidin-3-O-(6″-O-p-coumaroyl) glucoside being the highest relative content in the RDd. Differential metabolites were significantly enriched, mainly in flavonoid biosynthesis, anthocyanin biosynthesis, and flavone and flavonol biosynthesis pathways. Transcriptomic analysis revealed that high expression levels of structural genes for flavonoid and anthocyanin biosynthesis were the main reasons for color changes in D. devonianum stems. Based on correlation analysis and weighted gene co-expression network analysis (WGCNA) analysis, CHS2 (chalcone synthase) and UGT77B2 (anthocyanidin 3-O-glucosyltransferase) were identified as important candidate genes involved in stem pigmentation. In addition, key transcription factors (TFs), including three bHLH (bHLH3, bHLH4, bHLH5) and two MYB (MYB1, MYB2), which may be involved in the regulation of flavonoid biosynthesis, were identified. This study provides new perspectives on D. devonianum efficacy components and the Dendrobium flavonoids and stem color regulation.

Background: The bHLH genes play a crucial role in plant growth, development, and stress responses. However, there is currently limited research on bHLH genes in the important horticultural plant Rhododendron delavayi Franch. Methods: In this study, we conducted a comprehensive genome-wide identification and in-depth analysis of the bHLH gene family in R. delavayi using bioinformatics approaches. Results: A total of 145 bHLH family members were identified, encoding proteins ranging from 98 to 3300 amino acids in length, with molecular weights ranging from 11.44 to 370.51 kDa and isoelectric points ranging from 4.22 to 10.80. These 145 bHLH genes were unevenly distributed across 13 chromosomes, with three bHLH genes located on contig 52. Chromosome 8 contained the highest number of bHLH family members with 19 genes, while chromosomes 9 and 13 had the lowest, with 7 genes each. Phylogenetic analysis revealed a close evolutionary relationship between bHLH genes in R. delavayi and Arabidopsis thaliana. Subcellular localization analysis indicated that most bHLH genes were located in the nucleus. Promoter analysis of R. delavayi bHLH genes revealed the presence of various cis-regulatory elements associated with light responses, methyl jasmonate responses, low-temperature responses, and coenzyme responses, suggesting that bHLH genes are involved in multiple biological processes in R. delavayi. Through transcriptome analysis, we identified three key functional genes—Rhdel02G0041700, Rhdel03G0013600, and Rhdel03G0341200—that may regulate flower color in R. delavayi. Conclusions: In conclusion, our study comprehensively identified and analyzed the bHLH gene family in R. delavayi and identified three bHLH genes related to flower color, providing a foundation for molecular biology research and breeding in R. delavayi.

Rootstocks are vital in cucumber production. Although figleaf gourd (Cucurbita ficifolia) is among the species used, its application remains limited due to the perception that white-seeded pumpkin (C. maxima × C. moschata) offers superior commercial traits. This perception is partly due to the insufficient collection and evaluation of local figleaf gourd germplasm, which has obscured its potential as a rootstock. Based on prior screening, four wild figleaf gourd genotypes from Yunnan Province were selected and compared with seven commercial white-seeded pumpkin rootstocks. Scions grafted onto figleaf gourd exhibited vegetative growth (stem diameter, plant height, and leaf area) and fruit morphology (length, diameter, biomass, and surface bloom) comparable to the top-performing white-seeded pumpkin genotypes. Fruits from figleaf gourd rootstocks also displayed comparable or significantly higher nutritional quality, including vitamin C, total soluble solids, soluble sugars, and proteins. Notably, figleaf gourd itself showed significantly greater intrinsic resistance to Fusarium wilt than white-seeded pumpkin. When used as a rootstock, it protected the scion from pathogen stress by triggering a stronger antioxidant response (higher SOD and POD activity) and mitigating cellular damage (lower MDA levels and electrolyte leakage). These results provide evidence that these figleaf gourd genotypes are not merely viable alternatives but are high-performing rootstocks, particularly in enhancing nutritional value and providing elite disease resistance.

Background/Objectives: The 3-ketoacyl-CoA synthase (KCS) enzyme is a key and rate-limiting component in the biosynthesis of very long-chain fatty acids (VLCFAs). Through controlling VLCFA production, KCS plays an essential role in plant cuticle formation. The necrotrophic fungus Botrytis cinerea can infect all aboveground parts of rose plants (flowers, leaves, and stems), causing severe economic losses. KCS restricts pathogen invasion by influencing cuticle formation and enhances tolerance to environmental stresses. While the KCS gene family has been well-studied in some plants, it remains unexplored in rose (Rosa × hybrida Hort.), a species of significant ornamental and economic value. Methods: In this study, we conducted a genome-wide analysis of the RcKCS gene family in rose, identifying 18 non-redundant genes. Phylogenetic, structural, and synteny analyses were performed to investigate the evolutionary relationships, gene architecture, and duplication events. The expression patterns of RcKCS genes in rose petals during B. cinerea infection were examined, and transient overexpression and silencing of RcKCS6 were used to study its function. Results: RcKCS6 was found to be upregulated during gray mold infection, and transient overexpression reduced lesion size on infected petals. Conclusions: Our study provides the first comprehensive analysis of the RcKCS gene family in rose and highlights RcKCS6 as a potential candidate for improving resistance to gray mold in rose through molecular breeding.