Deep sequencing discovery of novel and conserved microRNAs in strawberry (Fragaria×ananassa)

In plants, microRNAs (miRNAs) play a critical role in post‐transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as Arabidopsis and rice. Deep sequencing technologies have facilitated identification of species‐specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. In this research, we used Solexa sequencing to discover new miRNAs in cultivated strawberry (Fragaria×ananassa). A total of 23 282 309 reads representing 22 500 402 distinct sequences were obtained from a short RNA library generated from small RNAs extracted from strawberry fruit tissues. On the basis of sequence similarity and hairpin structure prediction, we found that 156 639 reads representing 153 sequences have good matches to known miRNAs. We also identified 37 novel miRNA candidates. These sequences had not been previously described in other plant species. Potential target genes were predicted for the majority of and novel miRNAs. These results show that regulatory miRNAs exist in the agriculturally important cultivated strawberry and may play an important role in its growth, development and response to disease.