Independent evolution of miRNAs targeting orthologous genes – chance or necessity?

Independent evolution of miRNAs targeting orthologous genes – chance or necessity? LYDIA GRAMZOW, DAJANA LOBBES, GÜNTER THEIßEN Friedrich Schiller University Jena, Germany MicroRNAs (miRNAs) are small molecules that generally negatively regulate gene expression. They have been shown to have a faster birth and death rate than protein-coding genes. In plants, a famous hypothesis on how a miRNA can be born is the inverted duplication hypothesis, according to which a miRNA evolves by inverted duplication of its target gene. Here, we provide evidence for an origin by inverted duplication for the miRNAs miR444 and miR824. Using publicly available genome and transcriptome data, cloning strategies and detection of miRNAs by Northern blot hybridization, we elucidate that the miR444 originated early in the evolution of monocotyledonous plants while the miR824 evolved in Brassicaceae. For both miRNAs we show that, at least early in their evolution, these miRNAs and their target genes were in close proximity in the genome, indicating the origin by inverted duplication. Remarkably, both miRNAs target the same subfamily of MADS-box genes: AGL17-like genes encoding for transcription factors involved in root and shoot development. Only one out of more than a dozen other subfamilies of MADS-box genes in flowering plants is known to also be targeted by a miRNA. Hence, the question arises as to whether the regulation of AGL17-like genes by two different miRNAs in two different groups of flowering plants is more than chance. We will address this question in light of our current knowledge about AGL17-like genes.