Analysis of microRNAs and their targets from onion (Allium cepa) using genome survey sequences (GSS) and expressed sequence tags (ESTs)

Rukmini Mishra; Rupesh Mohapatra; Bijayalaxmi Mahanty; Raj Kumar Joshi

doi:10.6026/97320630015907

Analysis of microRNAs and their targets from onion (Allium cepa) using genome survey sequences (GSS) and expressed sequence tags (ESTs)

Bioinformation. 2019 Dec 31;15(12):907-917. doi: 10.6026/97320630015907. eCollection 2019.

Authors

Rukmini Mishra¹, Rupesh Mohapatra², Bijayalaxmi Mahanty³, Raj Kumar Joshi³

Affiliations

¹ School of Applied Sciences, Centurion University of Technology and Management, Odisha, India.
² Centre for Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751030, Odisha, India.
³ Dept. of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar-751022, Odisha, India.

Abstract

MicroRNAs are small non-coding RNAs of 21-24 nucleotides in length that acts as important modulators of gene expression related to numerous biological processes including development and defense response in eukaryotes. However, only a limited report on onion (Allium cepa) miRNAs is available and their associated role in growth and development of onion is not yet clear. Therefore, it is of interest to identify miRNAs and their targets in Allium cepa using the genome survey sequences (GSSs) and expressed sequence tags (ESTs) and deduce the functions of the target genes using gene ontology (GO) terms. We report 14 potential miRNAs belonging to 13 different families (miR162, miR168, miR172c, miR172e, miR398, miR400, miR414, miR1134, miR1223, miR6219, miR7725, miR8570, miR8703 and miR8752). BLAST analysis using psRNATarget server predicted 39 potential targets for the identified miRNAs majority of which were transcription factors implicated in plant growth, development, hormone signaling and stress responses. These data forms the basis for further analysis and verification towards understanding the miRNA mediated regulatory mechanism in Allium cepa.

Keywords: Allium cepa; ESTs; GSSs; gene ontology; miRNA targets; microRNA.