Long non-coding RNA-mediated competing endogenous RNA regulatory network during flower development and color formation in Melastoma candidum

Abstract

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.

Transcriptional convergence after repeated duplication of an amino acid transporter gene leads to the independent emergence of the black husk/pericarp trait in barley and rice

“…The significance of lncRNA in diverse biological processes is crucial in plant kingdoms, which can modulate the expression of target genes through cis ‐ and trans ‐acting mechanisms; impact the structure and function of chromatin; and participate in RNA transcription, splicing and stabilization (Zheng et al ., 2023 ). Several studies have illustrated the significance of lncRNAs in plant development and colour formation process (Li et al ., 2023 ; Zheng et al ., 2023 ). In this study, two Blp_lncRNAs were identified to be significantly co‐expressed with HvBlp , which may be involved in the stage‐ and tissue‐specific expression of HvBlp .…”

Whole-Transcriptome Sequencing Reveals That mRNA and ncRNA Levels Correlate with Pleurotus cornucopiae Color Formation

“…By constructing competitive endogenous RNA (ceRNA) networks of lncRNAs and circRNAs in mice with different coat colors, complex interactions between ncRNAs and messenger RNAs (mRNAs) related to skin and melanocyte development were discovered, which co-regulate pigmentation development [11]. Whole-transcriptome sequencing and broadly targeted metabolome analysis of circRNAs, mRNAs, and small RNAs (sRNAs) of Melastoma candidum at three different developmental stages led to the construction of nine circRNA-mediated ceRNA regulatory networks that demonstrated important roles in M. candidum flower development and color formation [12]. In fungi, ncRNAs, such as lncRNA and micro-RNA-like (milRNA) molecules are involved in cell division, nutrient perception, sexual reproduction, and other processes [13][14][15].…”