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

• Published in: Genes Vol. 13; no. 11; p. 2137
• Main Authors: Deng, Houyin, Huang, Rong, Hu, Dehuo, Wang, Runhui, Wei, Ruping, Yan, Su, Wu, Guandi, Sun, Yuhan, Li, Yun, Zheng, Huiquan
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 17.11.2022; MDPI
• Subjects: Analysis; bioinformatics; Chinese fir; Cloning; Conifers; Conserved sequence; Cunninghamia - genetics; Cunninghamia lanceolata; Datasets; evolution; Fertility; Flowers & plants; Free energy; Gene expression; Gene Expression Regulation, Plant; Genetic aspects; Gymnosperms; Humidity; Maximum likelihood method; Methods; MicroRNA; MicroRNAs; MicroRNAs - genetics; miRNA; miRNA resource; Phylogenetics; Phylogeny; Physiological aspects; Plant genetics; Plant growth; Plant reproduction; Plants, Genetically Modified - genetics; Protein structure; RNA sequencing; Secondary structure; Seeds; Software; Trees; China; United States > US; Chinese fir; evolution; free energy; miRNA resource; bioinformatics
• ISSN: 2073-4425; 2073-4425
• DOI: 10.3390/genes13112137

In this study, we aimed to expand the current miRNA data bank of Chinese fir ( (Lamb.) Hook.) regarding its potential value for further genetic and genomic use in this species. High-throughput small RNA sequencing successfully captured 140 miRNAs from a Chinese fir selfing family harboring vigor and depressed progeny. Strikingly, 75.7% (n = 106) of these miRNAs have not been documented previously, and most (n = 105) of them belong to the novel set with 6858 putative target genes. The new datasets were then integrated with the previous information to gain insight into miRNA genetic architecture in Chinese fir. Collectively, a relatively high proportion (62%, n = 110) of novel miRNAs were found. Furthermore, we identified one MIR536 family that has not been previously documented in this species and four overlapped miRNA families (MIR159, MIR164, MIR171_1, and MIR396) from new datasets. Regarding the stability, we calculated the secondary structure free energy and found a relatively low R value (R < 0.22) between low minimal folding free energy (MFE) of pre-miRNAs and MFE of its corresponding mature miRNAs in most datasets. When in view of the conservation aspect, the phylogenetic trees showed that MIR536 and MIR159 sequences were highly conserved in gymnosperms.