Abstract
To understand the molecular characteristics of the miR477 gene family of grape (Vvi-miR477) and to predict its target genes, the Vvi-miR477 genes were identified from previous small RNA sequencing data, then phylogenetic analysis and prediction of target gene were conducted. The Vvi-miR477 family consists of two precursor sequences and three mature sequences. The miR477 family members were mostly 19-22nt in length. The sequence is relatively conservative. Vvi-MIR477a and Vvi-MIR477b are located on chromosomes 1 and 2, respectively. These precursor sequences can form the typical stable stem-loop structure. Their minimum folding free energy is −39.10 kcal/mol and −50.90 kcal/mol, respectively. The MIR477 family can be divided into three groups. The prediction of target genes showed that Vvi-miR477 targets 26S proteasome, DEAD-box, GRAS family protein, Protein Phosphatase 2C, etc. The GO function of target genes was mainly enriched to six categories. The catabolic process, carboxylic ester hydrolase activity is shown to be high. This study provided a theoretical basis for further exploration of the molecular mechanism of miR477 in grape berry ripening.
Highlights
MicroRNAs are endogenous, non-coding singlestranded small RNA molecules with about 21–23 nucleotides, which are widely distributed in eukaryotes (Ye et al, 2019)
Acquisition of precursor and mature sequences of miR477 family members The family members, precursor and mature sequences of VvimiR477 were identified from previous small RNA sequencing data (Guo et al, 2018) through homologs searches of blast using already known miRNAs in other species according to the method of Xie et al (2010)
Analysis of the mature sequence and precursor sequence of the miR477 family The miR477 mature sequences of Vitis vinifera, Nicotiana tabacum, Malus domestica, Citrus sinensis, Manihot esculenta, Populus trichocarpa, Fragaria vesca, Physcomitrella patens, Lotus japonicus, Prunus persica, Solanum tuberosum, Aquilegia caerulea, Solanum lycopersicum, Asparagus officinalis, Gossypium raimondii, Amborella trichopoda, Carica papaya, Cucumis melo were subjected to multiple sequence alignment using CLUSTALW online software with the default parameters
Summary
MicroRNAs (miRNAs) are endogenous, non-coding singlestranded small RNA molecules with about 21–23 nucleotides, which are widely distributed in eukaryotes (Ye et al, 2019). A large number of studies have shown that miRNAs play a crucial role in regulating various metabolic and biological processes, including growth (Ding et al, 2020; LelandaisBrière et al, 2010), flowering time (Yang et al, 2019), sex determination (Sun, 2012), and phytohormone signaling (Liu and Chen, 2009). MiR172 regulates the development of Brassica napus flower organs by targeting the euAP2 gene (Wang et al, 2019). Auxin response factors of miR167 plays an important role in flower development and fertility of rice (Li et al, 2020b). The overexpression of miR319a reduced the transcription level of its targeted gene family TCP, significantly improved the trichome density of transgenic Populus tomentosa leaves, and relieved the harm of insect herbivores (Fan et al, 2020). Overexpression of miR399a could increase the content of soluble sugar, soluble solids, and vitamin C, indicating that the expression of miR399a is positively correlated with the
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