Expansion of the Human Micro RNA Gene Repertoire in the Human Lineage after the Divergence of Old World and New World Monkeys

Reiko F Kikuno

Abstract

It has been widely postulated that micro RNAs (miRNAs) have played an important role in achieving morphological complexity during the course of eumetazoan evolution, because the miRNA repertoire has continually increased along with greater complexity in the genomes of bilaterians and vertebrates. In particular, the miRNA repertoire is dramatically expanded in human. To examine how miRNAs changed during the process of primate evolution, we estimated the evolutionary origins of 1,527 present human miRNAs along the human lineage, after the divergence of eutherian mammals. We constructed an evolutionary profile of the miRNA genes, based on the presence and absence of the known and predicted functional orthologues in six non-human primate species: chimpanzee, gorilla, orangutan, gibbon, macaque, and marmoset and three representative eutherian mammals: bovine, dog and mouse. The functional orthologues were predicted by multiple genome sequence alignments and BLAST searches, followed by four filtering steps. The number of miRNA genes and gene families drastically expanded in the lineage of old world monkey, after the divergence from the common ancestor with new world monkey, at approximately seven-fold higher rates than the earlier stage of primate evolution. The rates of expansion of miRNA and gene families have been slightly declined in hominoids. Comparisons of the number of genes with that of the gene families acquired in each evolutionary period suggested that de novo gene generation, rather than gene duplication, considerably contributed to the generation of new miRNA genes.