Evolution of animal endogenous small RNAs by gene duplication mechanisms

Abstract

Small regulatory RNAs have arisen as the most crucial class of regulatory elements that drove complexity in the evolution of plants and animals. Their nature that controls their targets by simple sequence complementarity allowed them to introduce hugely diverse biological characteristics in relatively short time of evolution. While the origins of plant microRNA (miRNA) and siRNA have been hypothesized and slightly validated by several scientists, those of animal’s are barely studied yet due to their somewhat indiscriminating recognition of targets. In this study, I examine how many animal miRNAs have been emerged according to hypothesized scenarios. Inverted repeat duplicated from target gene and random sequences introduced by transposable elements are the well-known hypothetic origin of plant miRNA. As transposable elements’(TE) being a reservoir of regulatory element shuffling, TE can give another consequence for de novo miRNA-mRNA pair formation: 3’UTR region of a coding gene is contaminated, then an instance of TE is evolved into a miRNA gene. Recently, pseudogene-derived siRNA is also begun to be thought as a intermediate stage to complete miRNA gene. A miRNA gene might be generated by evolution of the hpRNA that had encoded an endogenous siRNA. I discover small RNA loci that are identifiable as evolved by the scenarios in the genomes of twelve Drosophila clades. My study presents several refined computational methods, for identifying and testing potential genes for the hypotheses, which is tuned to work with the animal genome. Also, this study clarifies that the gene duplication mechanisms have been important to emergence of new miRNA genes in the animal genome.