Abstract
In plants there are several classes of 21-24 nucleotide short RNAs that regulate gene expression. The most conserved class is the microRNAs (miRNAs), although some of the miRNAs were found only in specific species. We used high throughput pyrosequencing to identify conserved and non-conserved miRNAs and other short RNAs in tomato fruit and leaf. Several conserved miRNAs showed tissue specific expression, which, combined with target gene validation results, showed that fleshy fruit development is regulated by miRNAs. We also identified four new non-conserved miRNAs. One of the validated targets of a novel miRNA is a member of the CTR transcription family involved in fruit ripening. However, 62 predicted targets showing near perfect complementarity to potential new miRNAs did not validate experimentally. This demonstrates that target prediction of plant short RNAs has a high rate of false positives and must be validated experimentally. We also found short RNAs from a Solanaceae specific foldback transposon, which showed a miRNA/miRNA* like distribution suggesting that this element may function as a miRNA gene progenitor. The other Solanaceae specific class of short RNA was derived from an endogenous pararetrovirus sequence inserted into the tomato chromosomes. This study opens a new avenue in the field of fleshy fruit biology by demonstrating that fruit development and ripening is under miRNA regulation.