Journal Article

Integrated microRNA and whole-transcriptome sequencing reveals the involvement of small and long non-coding RNAs in the fiber growth of ramie plant

Yi, Langbo, Rao, Jing, Liu, Chan, Fu, Yafen, Yang, Xiai, Wang, Yanzhou, Zhu, Siyuan, Li, Fu, Liu, Touming

2023

Overview

Background MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are the two main types of non-coding RNAs that play crucial roles in plant growth and development. However, their specific roles in the fiber growth of ramie plant ( Boehmeria nivea L. Gaud) remain largely unknown. Methods In this study, we performed miRNA and whole-transcriptome sequencing of two stem bark sections exhibiting different fiber growth stages to determine the expression profiles of miRNAs, lncRNAs, and protein-encoding genes. Results Among the identified 378 miRNAs and 6,839 lncRNAs, 88 miRNAs and 1,288 lncRNAs exhibited differential expression. Bioinformatics analysis revealed that 29 and 228 differentially expressed protein-encoding genes were targeted by differentially expressed miRNAs and lncRNAs, respectively, constituting eight putative competing endogenous RNA networks. lncR00022274 exhibited downregulated expression in barks with growing fibers. It also had an antisense overlap with the MYB gene, BntWG10016451 , whose overexpression drastically increased the xylem fiber number and secondary wall thickness of fibers in the stems of transgenic Arabidopsis , suggesting the potential association of lncR00022274- BntWG10016451 expression with fiber growth. Conclusions These findings provide insights into the roles of ncRNAs in the regulation of fiber growth in ramie, which can be used for the biotechnological improvement of its fiber yield and quality in the future.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Animal Genetics and Genomics / Arabidopsis thaliana / Bark / Bioinformatics / Biomedical and Life Sciences / Biosynthesis / Biotechnology / Cellulose / Composition / Diseases and pests / DNA sequencing / Enzymes / Fiber growth / Fibers / Gene expression / Genes / Genetic aspects / Genetic engineering / Genetic transcription / Genomes / Genomics / Growth / Life Sciences / Lignin / Long non-coding RNA / Methods / Microarrays / Microbial Genetics and Genomics / MicroRNA / MicroRNAs / miRNA / MYB gene / MYB transcriptional factor / Non-coding RNA / Nucleotide sequencing / Plant fibers / Plant Genetics and Genomics / Plant growth / Polymerization / Proteins / Proteomics / Ramie / Ribonucleic acid / RNA / Small RNA / Stems / Toiletries industry / Transcription factors / Transcriptomes / Xylem