mirMachine: a one-stop shop for plant miRNA annotation

Authors: CAGIRICI, BUSRA - Oak Ridge Institute For Science And Education (ORISE); Sen, Taner; BUDAK, HIKMET - Montana Bioagriculture Inc

Submitted to: The Journal of Visualized Experiments (JoVE)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/6/2021
Publication Date: 5/1/2021
Citation: Cagirici, B.H., Sen, T.Z., Budak, H. 2021. mirMachine: a one-stop shop for plant miRNA annotation. The Journal of Visualized Experiments (JoVE). (171). Article e62430. https://www.doi.org/10.3791/62430.
DOI: https://doi.org/10.3791/62430

Interpretive Summary: Among the non-coding ribonucleic acids (RNAs) in the cell, small RNAs called microRNAs or miRNAs, that are around 22-nucleotide long were demonstrated to play crucial roles in cellular control and regulation mechanisms that have direct impact on how cells respond to environmental conditions such as drought and diseases. With the availability of fully sequenced genome assemblies, such as Chinese Spring wheat, we developed a computational pipeline called the SUmir pipeline that consists of (1) the SUmir miRNA identification program that can be downloaded and run on a local machine to predict miRNAs and (2) the SUmirFold program to predict miRNA secondary structures. As a proof-of-concept, the SUmir pipeline was applied to the Chromosome 5A of the International Wheat Genome Sequencing Consortium's Chinese Spring wheat assembly. All scripts and programs that are part of the SUmir pipeline are made freely and publicly available.

Technical Abstract: Of different types of noncoding RNAs, microRNAs (miRNAs) have arguably been in the spotlight over the last decade. As post-transcriptional regulators of gene expression, miRNAs play key roles in various cellular pathways, including both development and response to a/biotic stress, such as drought and diseases. Having high quality reference genome sequences enabled identification of miRNAs in several plant species, where miRNA sequences are highly conserved. Since computational miRNA identification processes are mostly error prone processes, homology based predictions still stand as viable approaches given the highly conserved genomes of plants. We developed the SUmir pipeline and improved during the last decade and SUmir has been used for variety of plant genomes since then. In this study, we upgraded the SUmir pipeline by (i) an additional filtering step on the secondary structure predicted by SUmirFold, (ii) making whole pipeline freely available, and (iii) making it fully automated. The new and updated miRNA annotation pipeline, the SUmir pipeline, was tested on the chromosome 5A of the IWGSC wheat reference genome assembly v2. The SUmir pipeline will be freely available.