RNA-Seq Data Analysis Unveils Potential Conserved Micro-RNAs in Agave Deserti

Abstract

Exploring molecular mechanism of abiotic stress tolerance in plants is needed to overcome the deterioration of yield and quality of crop plants to meet the food security challenges of the growing population. MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate target gene expression for modulating plant growth, development, and response to different stresses. Agave belonging to CAM plants’ has remarkable tolerance to extreme conditions of drought and heat; however, molecular mechanisms underlying this excellence are yet to explore. This study applies comparative genomics approach on available Transcriptome (RNA- Seq) data of Agave deserti to identify potential miRNAs, and miRNA targets. Transcriptome datasets consisting of 128,869 Agave contigs was processed to create local database, for nucleotide homology analysis with 6,028 non-redundant plant miRNAs as query sequences. Protein coding sequences were removed, and potential pre-miRNA sequences were tested for stability analysis based on a variety of factors, including but not limited to %G+C content and minimum free energy (-ΔG), as a filter to remove pseudo pre-miRNAs. This study identified 30 unique miRNAs of Agave deserti harboring 14 different categories of precursors. Phylogenetic analysis revealed evolutionary relationship between newly identified pre-miRNAs with corresponding pre-miRNA homologues. Target genes of miRNAs were predicted subsequently, and possible functions were defined by functional annotation analysis. The results of this study will pave the way for further research, exploring the molecular mechanisms in Agave deserti and the role of miRNAs in gene regulation under abiotic stresses.