Identification of grapevine microRNAs and their targets using high throughput sequencing and degradome analysis.

In plants, microRNAs (miRNAs) comprise one of three classes of small RNAs regulating gene expression at post-transcriptional level. Many plant miRNAs are conserved and play a role in development, abiotic stress responses or pathogen responses. However, some miRNAs have been found only in certain species. Here, we use deep sequencing, computational and molecular methods to identify, profile and describe conserved and non-conserved miRNAs in four grapevine (Vitis vinifera) tissues. 24 conserved miRNA families were identified in all four tissues and 26 known but non-conserved miRNAs were also found. In addition to known miRNAs we also found 21 new grapevine specific miRNAs together with their star strands. We have also shown that almost all of them originated from single genes. Furthermore, 21 other plausible miRNAs candidates have been described. We have found that many known and new miRNAs showed tissues-specific expression. Finally, 112 target mRNAs of known and 44 target mRNAs of new grapevine specific miRNAs were identified by genomic scale high-throughput sequencing of miRNA cleaved mRNAs.