Identification And Analysis Of Single Nucleotide Polymorphisms In MicroRNAs Of Arabidopsis Thaliana

MicroRNAs are endogenous small regulatory non-coding RNAs and organized in different families.Since microRNAs plays an important role in various physiological processes,the single nucleotide mutations of pre-miRNA can affect the maturation process and regulation function of microRNA.Therefore,it is important to study the distribution of single nucleotide polymorphism(SNP)in microRNA genes,which is significant for the understanding of functional differentiation and gene evolution of microRNA.With the rapid development of high-throughput sequencing technology and bioinformatics technology,SNP events on the microRNA sequences are identified in a large number of animals.As a model plant,a large scale of small RNA sequencing data has been generated in Arabidopsis thaliana,but the studies of SNP events in the microRNAs has been reported little.In this study,we used a large number of Arabidopsis small RNA sequencing data from NCBI,with the analysis method of MiRME and SNP information from dbSNP about Arabidopsis thaliana,to study the SNPs events and analysis the SNP feature and its impact on microRNA function.The main results are as follows:(1)In the dbSNP database,1069109 SNP loci were identified,and 693 SNP events occurred in the microRNA sequences,which contained 91 SNP events in the mature sequence region of microRNAs.In these SNP events,there are 41 SNP events occurred in the conserved microRNA sequence.By classification these SNP sites with the mutation type,we found that there were 142 G to A sites,62 A to G sites,105 C to U sites,99 U to C sites,the number of other types of SNP events are relatively few.(2)By analysis of the 100 collecting Arabidopsis smallRNA sequencing data,a total of 74 significant SNP loci(Cor_p_value ? 0.05)occurred in the microRNA sequences,which had 12 SNP sites was collected in the dbSNP database.(3)To predict the target genes of mature microRNA sequence with SNP sites on it,and it was found that the occurrence of SNP had an important influence on the number and species of the target genes of microRNA.(4)To predict the secondary structure of microRNA sequence with SNP sites on it,and it was found that the influence of SNP for the stability of the secondary structure was related to the location of the SNP locus and the base type of the mutation.(5)We studied the GO function enrichment analysis for the target genes of microRNA with SNP,and found that the occurrence of SNP event had a significant impact on the GO enrichment of microRNA target genes.