Comparative genome analyses for discovery of RNA silencing networks in plant innate immunity

We discovered a class of structurally and functionally unique microRNAs that silence and regulate plant innate immune receptor genes (resistance (R) genes) in three Solanaceae species –tobacco, tomato, and potato. These novel miRNAs target receptor gene transcripts for cleavage and trigger production of a second group of silencing small RNAs from “sliced” transcripts. We recently identified a new class of miRNAs that silence the structurally conserved family of R-genes encoding leucine rich repeat receptor-like protein (RLP) genes. We show that this new class of miRNAs are derived from ancestral RLP gene fragments arranged as long inverted repeats in the 3’ UTRs of four different and unrelated expressed genes and that RLP-miRNA biogenesis is dependent on Dicer-like 4 (DCL4). Using comparative genomics, visualized in the Maverix genome browser, we found that the predicted protein coding regions and 3’UTRs of the miRNA precursor genes are conserved in tomato, potato and tobacco suggesting a possible relationship between expression of these genes and RLP-mediated disease resistance. This miRNA regulatory system has broader mechanistic and evolutionary implications for understanding evolution of silencing networks for regulation of gene families and or genes evolving through positive selection imposed by biotic or abiotic environmental pressure. miRNAs are regulators of several fundamental processes in higher eukaryotes, and this work demonstrates that regulation of agronomically significant innate immune receptor genes and their encoded cell-death response is another miRNA-regulated process. The wide distribution of plant miRNAs targeting innate immune receptor genes suggests that this two-part silencing system is a conserved mechanism.