Identification and characterization of tissue specific microRNAs in chickpea by high-throughput sequencing

Abstract

Chickpea (Cicer arietinum) is the most important pulse crop in the Indian subcontinent. MicroRNAs (miRNAs) are essential components of complex gene regulatory networks that are involved in plant development. In the current study, miRNAs from leaf and root tissues were identified from chickpea. Computational analysis of small RNA sequences obtained using Illumina Genome analyser led to identification of total of 368 miRNAs. 24 families consisting of 97 conserved miRNAs and 73 novel miRNAs were identified in root and leaf tissues after extensive sequence analysis. Poly(A)-based qRT-PCR (Quantitative real-time PCR) expression analysis of several miRNAs was done for leaf and root tissues of chickpea. Nine conserved and 3 novel miRNA were found to be differentially expressed between leaf and root tissues. The target genes of all the identified miRNAs were predicted by psRNATarget web server using chickpea transcriptome database. The predicted target genes (approximately 358 different transcripts) were extensively involved in different biological processes involving a large number of gene families. This study has identified several conserved and novel miRNAs along with their expression profiling and has predicted several target genes and thereby lays the foundation for studies on gene regulation in response to chickpea development.