Global non-random abundance of short tandem repeats in rodents and primates

Abstract

AbstractBackgroundWhile of predominant abundance across vertebrate genomes and significant biological implications, the relevance of short tandem repeat (STR) abundance to speciation remains largely elusive and attributed to random coincidence for the most part. In a model study, here we collected whole-genome abundance of mono-, di-, and trinucleotide STRs in nine species, encompassing rodents and primates, including rat, mouse, olive baboon, gelada, macaque, gorilla, chimpanzee, bonobo, and human. The obtained unnormalized and normalized data were used to analyze hierarchical clustering of the STR abundances in the selected species.ResultsWe found massive differential abundances between the rodent and primate orders. In addition, while numerous STRs had random abundance across the nine selected species, the global abundance conformed to three consistent <clusters>, as follows: <rat, mouse>, <gelada, macaque, olive baboon>, <gorilla, chimpanzee, bonobo, human>, which coincided with the phylogenetic distances of the selected species (p< 4E-05). Exceptionally, in the trinucleotide STR compartment, human was significantly distant from all other species.ConclusionWe propose that the global abundance of STRs is non-random in rodents and primates, and probably had a determining impact on the speciation of the two orders. We also propose the STRs and STR lengths which specifically coincided with the phylogeny of the selected species.