Conserved microRNAs and their targets in rubber tree and the related Euphorbiaceous species

Plant microRNAs (miRNAs) have been demonstrated to play an important regulatory role in a variety of biological processes ranging from plant growth and development, defensive pathways, as well as biotic and abiotic stress responses. MiRNAs have been extensively studied in plant models with available genome sequence data. The Euphorbiaceae family is a large flowering plant family, which is of considerable economic importance, but relatively limited genome sequence data. The four Euphorbiaceous species; rubber tree, cassava, castor bean and leafy spurge; were selected for this study. Using conserved plant miRNAs sequences aligned to the GenBank expressed sequenced tag database of each target plants, and further potential precursor miRNA-secondary structure analysis, the 526 potential miRNAs belonging to 17 miRNA families and their targets were identified. The majority of miRNA families was able to be identified in cassava. The minimal folding free energy index of precursor miRNAs was significantly higher than other non-coding or coding RNAs. The largest group of miRNA target genes consists of regulatory genes predicted to encode transcription factors, while non-regulatory genes involving in various functions. Some miRNAs contain different targets, suggesting the diverse functions of miRNAs depending on plant species and environmental conditions. The 6 expressed Hbr-miRNAs were verified in rubber tree. Gaining insight into the miRNA targets will help us to understand the range of miRNA expression regulation and to more coherently describe the functional importance of miRNAs. These findings considerably facilitate the basis for broaden future investigation on the role of these miRNAs in the economic important Euphorbiaceous species.