M. candidum, an evergreen shrubby flower known for its superior adaptation ability in South China, has gained increased attention in garden applications. However, scant attention has been paid to its flower development and color formation process at the non-coding RNA level. To fill this gap, we conducted a comprehensive analysis based on long non-coding RNA sequencing (lncRNA-seq), RNA-seq, small RNA sequencing (sRNA-seq), and widely targeted metabolome detection of three different flower developmental stages of M. candidum. After differentially expressed lncRNAs (DElncRNAs), differentially expressed mRNAs (DEmRNAs), differentially expressed microRNAs (DEmiRNAs), and differentially synthesized metabolites (DSmets) analyses between the different flower developmental stages, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted to identify some key genes and metabolites in flavonoid, flavone, anthocyanin, carotenoid, and alkaloid-related GO terms and biosynthetic pathways. Three direct-acting models, including antisense-acting, cis-acting, and trans-acting between lncRNAs and mRNAs, were detected to illustrate the direct function of lncRNAs on target genes during flower development and color formation. Based on the competitive endogenous RNA (ceRNA) regulatory theory, we constructed a lncRNA-mediated regulatory network composed of DElncRNAs, DEmiRNAs, DEmRNAs, and DSmets to elucidate the indirect role of lncRNAs in the flower development and color formation of M. candidum. By utilizing correlation analyses between DERNAs and DSmets within the ceRNA regulatory network, alongside verification trials of the ceRNA regulatory mechanism, the study successfully illustrated the significance of lncRNAs in flower development and color formation process. This research provides a foundation for improving and regulating flower color at the lncRNA level in M. candidum, and sheds light on the potential applications of non-coding RNA in studies of flower development.

The MYB gene family is significant in plants, playing a role in numerous plant development processes, including metabolism, hormone signal transduction, cell identity, and biotic and abiotic stresses. Due to the recent availability of the Melastoma candidum genome, this is the first time that the MYB gene family has been identified in this species. This study identified 421 MYB gene members in the M. candidum genome using the HMMER search and BLASTp method. These MYBs were further divided into 10 sub-types, including R2R3, R-R, CPC-like, CCA1-like, TBP-like, R1R2R3, I-box, atypical MYB, MYB-CC, and MYB-like. Domain and conservation analyses revealed that each type of MYB was characterized by a different number and combination of SANTs/myb DNA-binding domains. Collinearity analysis revealed several gene duplication events within the MYB gene family. The Ka to Ks ratio suggested that most of the MYB genes underwent purifying selection during the evolution process. Phylogenetic analysis among three species confirmed our findings and displayed the evolutionary relationship of MYB genes in different species. RNA-seq of three developmental stages of flowers and WGCNA analysis identified McMYB113h, McMYB21b, and McGLK1c as playing a pivotal role during flower development in M. candidum. Finally, we conducted qRT-PCR experiments for 20 flower-development-related MYBs across 9 tissues to illustrate their expression patterns in M. candidum. This study establishes a foundation for exploring MYB gene resources and their potential applications in related industries of M. candidum.

Bougainvillea peruviana is a widely domesticated ornamental plant species. However, studies on B. peruviana are limited. In this study, we reported the complete chloroplast (cp) genome of B. peruviana. The cp genome is 154,465 bp in length, containing a large single-copy (LSC) of 85,563 bp and a small single-copy (SSC) of 18,050 bp, which are separated by a pair of inverted repeats (IRs) of 25,426 bp, each. A total of 132 genes, including 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes, were predicted. The overall GC content for the cp genome is 36.5%. The maximum-likelihood tree constructed based on cp genome sequences showed that B. peruviana is placed under Nyctaginaceae and is diverged before Bougainvillea glabra and Bougainvillea spectabilis under strong bootstrap support.