Mining of miRNAs in pomegranate (Punica granatum L.) by pyrosequencing of part of the genome

Abstract

Plant microRNAs (miRNAs) are short, non-coding, conserved RNAs that play an important role in the transcriptional and post-transcriptional regulation of gene expression. Five miRNAs were identified in pomegranate (Punica granatum L.) using a bioinformatics approach on 7,361 contigs from partial genome sequence data (19 Mbp) generated using Roche 454 GS FLX Titanium pyrosequencing technology. Thirty-five potential mRNA targets were identified by homology searches of all five identified pomegranate miRNAs against the Arabidopsis thaliana mRNA dataset using psRNAtarget software (http://plantgrn.noble.org/psRNATarget/). The miRNA targets identified were then subjected to Gene Ontology analysis. We found that most mRNA targets were constitutively expressed genes involved in different molecular functions, biological processes, and cellular components. Experimental validation of these computationally-identified miRNAs has the potential to elucidate miRNA-based gene regulation and evolution in a non-model crop such as pomegranate.