Genome-wide identification and expression profiling of microRNAs genes during SE and in different organs/tissues in Dimocarpus longan Lour.
Abstract Background MicroRNAs (miRNAs) is a conserved class of single-stranded noncoding RNAs, which regulate growth and development, hormone response, and stress responses in plant. Longan (Dimocarpus longan Lour.) is an important fruit tree with medicinal value and considerable economic value. However, there is no research on genome-wide identification of miRNAs genes in longan.Results Here, we conducted a genome-wide survey of longan miRNA genes, characterizing their structure and expression. A total of 88 miRNA precursors comprised of 30 known miRNA families and three undefined miRNA families were obtained. Of the 30 known longan miRNA families, 16 were represented by multiple loci in longan genome, which were also found more diverse in genome loci numbers in other plants; and four of them, involving miR395, -399, -477, and -3627 families, were identified as miRNA clusters genes; Among the 16 miRNA families, the conserved region as mature miRNA, as would be expected, and the loop region sequences of miRNA genes were divergent. Further, amplification and characterization of the longan pri-miRNA genes were carried out, and the upstream transcription 5 'region of 19 miRNAs and the downstream transcription 3' region of 12 miRNAs with typical poly (a) tails were obtained, showing that longan miRNAs genes possess multiple transcription start sites (TSSs) or polymorphism trait, suggesting pri-miRNA has similar transcription specialty as protein-encoding genes. Subsequently, promoter cis-element analysis on longan miRNA genes showed that the top three most abundant cis-elements were light-responsive elements, stress- responsive elements, and hormone responsive elements. Quantitative real-time PCR showed that pre-miRNAs were differentially expressed during the early stages of longan somatic embryogenesis, and the most number of highly expressed pre-miRNAs were detected in anther samples in different organs/tissues types of longan,Conclusion This is the first report concerning genome-wide identification and expression profiling of microRNAs genes, and will serve as a foundation for future research into the functional roles of miRNA genes in longan.