Origins and Evolution of MicroRNA Genes in Drosophila Species

Abstract

MicroRNAs (miRs) regulate gene expression at the posttranscriptional level. To obtain some insights into the origins and evolutionary patterns of miR genes, we have identified miR genes in the genomes of 12 Drosophila species by bioinformatics approaches and examined their evolutionary changes. The results showed that the extant and ancestral Drosophila species had more than 100 miR genes and frequent gains and losses of miR genes have occurred during evolution. Although many miR genes appear to have originated from random hairpin structures in intronic or intergenic regions, duplication of miR genes has also contributed to the generation of new miR genes. Estimating the rate of nucleotide substitution of miR genes, we have found that newly arisen miR genes have a substitution rate similar to that of synonymous nucleotide sites in protein-coding genes and evolve almost neutrally. This suggests that most new miR genes have not acquired any important function and would become inactive. By contrast, old miR genes show a substitution rate much lower than the synonymous rate. Moreover, paired and unpaired nucleotide sites of miR genes tend to remain unchanged during evolution. Therefore, once miR genes acquired their functions, they appear to have evolved very slowly, maintaining essentially the same structures for a long time.

Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry

“…This is in general much lower than the clustered MIRNAs in human and Drosophila spp. (approximately 40%; Altuvia et al, 2005;Nozawa et al, 2010). The two miRFBX clusters found in F. vesca demonstrated that the relatively large size of the MIRNA gene family could arise quickly from tandem duplications, even though this is rather rare in plants.…”

Systematic analysis of human microRNA divergence based on evolutionary emergence

“…The phylogenetic distribution and evolution of animal and plant miRNAs have been studied in recent reports [2][3][4][5][6][7][8][9][10][11][12]. In animals, the expansion of miRNAs is an ongoing process [5].…”

Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems

“…Other ways that new miRNAs can arise include the modification or duplication of pre-existing miRNAs [108]. A rapid increase in the diversity of miRNAs in existing genomes is often correlated to a burst of new morphological diversity, and thus miRNA may be crucial to the development of complex morphologies because of its regulatory activity [71,110,134].…”

“…However archaic miRNAs often have an extremely slow rate of mutation, which suggests that the miRNA undergoes purifying selection. Once an miRNA has gained a function, it rarely is lost from the genome [108,110]. Because older miRNAs evolve at a very low rate, and as a result are well conserved, they can be used as excellent phylogenetic markers [134].…”