Characterization of conserved microRNAs from five different cucurbit species using computational and experimental analysis

MicroRNAs (miRNAs) are ∼21 nt non-coding small RNAs which regulate gene expression at the post-transcriptional level in plants and animals. Until recently, only limited numbers of miRNAs were identified in Cucurbitaceae, a large flowering plant family. In this study, 220 potential miRNA candidates were identified from five species of Cucurbitaceae family using a comparative genome-based computational analysis. A comprehensive bioinformatic analysis of EST (expressed sequence tag) and GSS (genomic survey sequence) data of five cucurbit species showed that at least 41, 108, 21, 17 and 33 miRNAs existed in Cucumis sativus, Cucumis melo, Citrullus lanatus, Siraitia grosvenorii and Cucurbita pepo, respectively. Quantitative real-time PCR (qRT-PCR) analysis revealed the differentially expression levels of miRNAs in the four tissues of cucumber and melon. These identified miRNAs in the five species potentially targeted 578 protein-coding genes and one target of the C. melo miRNA cme-miR160a-5p was verified by 5′ RLM-RACE. GO and KEGG analysis suggested that many melon miRNAs might involve in nucleotide metabolism, oxidative phosphorylation, cell redox homeostasis and signal transduction.