Profiling of Novel and Candidate microRNAs in Grapevine By High Throughput Sequencing

Genetic and epigenetic gene regulations are crucial in understanding many aspects of plant development and we addressed these issues focusing on microRNAs (miRNAs).  Plant miRNAs are a family of 21 or 22 nt small RNAs molecules that modulate gene expression in a post-transcriptional manner by down-regulating target gene products involved in several cellular processes. To date, a relatively large number of grapevine miRNAs are deposited in miRBase and reported in the literature, but all are limited in scope to a few cell types/organs and developmental stages. Focusing on the identification of novel miRNAs in Vitis vinifera cv. Corvina, here we describe the results obtained by deep sequencing 68 small RNA libraries constructed using 34 different tissues at different developmental stages. A total of 49 new miRNA candidates from 52 precursors and 34 new variants of known miRNAs from 42 precursors were identified. The expression patterns of these miRNAs candidates were analyzed. Interestingly, some of the new candidates were found to be preferentially expressed in a particular tissue or developmental stage. This study is the first genome-wide study combining high-throughput, computational and statistical approaches for the identification of miRNAs and analysis of their expression pattern in grapevine. Expression data will be integrated with results of target genes identification experiments to describe these miRNA candidates’ functional roles.