Tomato MicroRNAs and Their Functions.

MicroRNAs (miRNAs) define an essential class of non-coding small RNAs that function as posttranscriptional modulators of gene expression. They are coded by genes, several hundreds of which exist in the genomes of Arabidopsis and rice model plants. The functional analysis of Arabidopsis and rice miRNAs indicate that their miRNAs regulate a wide range of processes including development, reproduction, metabolism, and stress. Tomato serves as a major model crop for the study of fleshy fruit development and ripening but until recently, information on the identity of its genes and their coded miRNAs was limited and occasionally contradictory. As a result, the majority of tomato miRNAs remained uncharacterized. Recently, a comprehensive annotation of tomato genes has been carried out by several labs and us. In this review, we curate and organize the resulting partially overlapping annotations into an exhaustive and non-redundant atlas of tomato genes. There are 538 candidate and validated genes in the atlas, of which, 169, 18, and 351 code for highly conserved, -specific, and tomato-specific miRNAs, respectively. Furthermore, a critical review of functional studies on tomato miRNAs is presented, highlighting validated and possible functions, creating a useful resource for future tomato miRNA research.