Biomics

MicroRNAs are small non-coding RNA molecules that act as post-transcriptional regulators of gene expression due to rather strict complementarity to their mRNA and have a length of 20-24 nucleotides. Plant microRNAs control a wide range of physiological processes, including nutrition, growth, resistance reactions and interaction with other organisms, via modulation of the expression of transcription factors, stress-induced proteins, hormone biosynthesis enzymes, and other genes. Legumes are able to form mutualistic symbioses simultaneously with nitrogen-fixing bacteria and arbuscular mycorrhiza. Both the early and late stages of these symbiosis are regulated by complex genetic mechanisms. As it has become known in recent years, one of these mechanisms is the regulation of gene expression by microRNA. The study of microRNAs is carried out by various methods, but over the past decade, next-generation sequencing (NGS) technologies have become the most popular approach in this field. NGS is used to identify conservative and novel microRNAs in the genomes of various organisms (both model and nonmodel), as well as to study the functioning of microRNAs in various experimental conditions with the additional use of transcriptome and degradome sequencing data. The article describes the main stages of working with microRNA sequencing data: quality control of reads (with a list of programs required at this stage), identification of conservative and novel microRNAs using miRDeep2 tool, search for targets of identified microRNAs using PAREsnip2, functional annotation of targets and the use of statistical tests for the analysis of functional enrichment, which facilitates the interpretation of the data obtained and allows us to make assumptions about the biological consequences of the activity of identified microRNAs in the object under study. This information may be useful for researchers who deal with microRNAs in silico for the first time or want to save time and resources on searching and analyzing information about the tools needed to work with microRNA sequencing data.

Plants, root symbiosis, microRNAs, Next-Generation Sequencing, degradome

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