Uncovering miRNA-mRNA Regulatory Modules in Developing Xylem of Pinus massoniana via Small RNA and Degradome Sequencing

Abstract

Xylem is required for the growth and development of higher plants to provide water and mineral elements. The thickening of the xylem secondary cell wall (SCW) not only improves plant survival, but also provides raw materials for industrial production. Numerous studies have found that transcription factors and non-coding RNAs regulate the process of SCW thickening. Pinus massoniana is an important woody tree species in China and is widely used to produce materials for construction, furniture, and packaging. However, the target genes of microRNAs (miRNAs) in the developing xylem of P. massoniana are not known. In this study, a total of 25 conserved miRNAs and 173 novel miRNAs were identified via small RNA sequencing, and 58 differentially expressed miRNAs were identified between the developing xylem (PM_X) and protoplasts isolated from the developing xylem (PM_XP); 26 of these miRNAs were significantly up-regulated in PM_XP compared with PM_X, and 32 were significantly down-regulated. A total of 153 target genes of 20 conserved miRNAs and 712 target genes of 113 novel miRNAs were verified by degradome sequencing. There may be conserved miRNA-mRNA modules (miRNA-MYB, miRNA-ARF, and miRNA-LAC) involved in softwood and hardwood formation. The results of qRT-PCR-based parallel validation were in relatively high agreement. This study explored the potential regulatory network of miRNAs in the developing xylem of P. massoniana and provides new insights into wood formation in coniferous species.

Exploring the Seasonal Dynamics and Molecular Mechanism of Wood Formation in Gymnosperm Trees

“…miR165 induces SCW in pith by downregulating AtHB15 in Arabidopsis [75]. The miRNA transcriptional profile of xylem during different stages of SCW formation has been studied in Chinese red pine [15]. Like hormonal and genetic regulation, regulation by miRNAs is also seasonal, as first reported by Ko et al [74].…”

“…Non-coding RNAs are involved in the epigenetic regulation of wood formation [14][15][16]. MicroRNAs (miRNAs), which are 20 to 24 nucleotides in length, are widely recognized as one of the major epigenetic regulating factors [17,18].…”

Integrated SMRT and Illumina Sequencing Provide New Insights into Crocin Biosynthesis of Gardenia jasminoides

“…Numerous studies have also revealed the role of lncRNAs in plant secondary metabolites. Lignin is one of the major components of wood and one of the important renewable energy sources on Earth [ 43 , 44 ]. Quan et al found that some lncRNAs may regulate some protein-coding genes in the lignin biosynthesis pathway in a cis or trans manner, providing new insights into wood formation [ 45 ].…”

Further Mining and Characterization of miRNA Resource in Chinese Fir (Cunninghamia lanceolata)

“…The conifers are expected to provide important information regarding the evolution of highly conserved small regulatory RNAs [ 8 ]. An increasing number of miRNAs studies about growth and development are being carried out in coniferous trees from different genus, such as Pinus L. [ 8 , 9 , 10 , 11 ], Picea A. Dietrich [ 12 ], Araucaria Juss. [ 13 ] and Ginkgo L. [ 14 ].…”