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

Abstract

Background: While of predominant abundance across vertebrate genomes and significant biological implications, the relevance of short tandem repeats (STRs) (also known as microsatellites) to speciation remains largely elusive and attributed to random coincidence for the most part. Here we collected data on the 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 collected data were used to analyze hierarchical clustering of the STR abundances in the selected species.

Results: We found massive differential STR 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>, and <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.

Conclusion: Based on hierarchical clustering, we 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 predominantly conformed to the phylogeny of the selected species, exemplified by (t)10, (ct)6, and (taa4). Phylogenetic and experimental platforms are warranted to further examine the observed patterns and the biological mechanisms associated with those STRs.

Keywords: Abundance; Global; Hierarchical clustering; Non-random; Primate; Rodent; Short tandem repeat.

Fig. 1

Whole-genome mononucleotide STR abundance in the nine selected species. Global incremented pattern was observed in the primate species versus rodents (left graph). The overall hierarchical clustering yielded three , which conformed to , , and (right graph).

Fig. 2

Whole-genome dinucleotide STR abundance in the nine selected species. Global decremented patterns were observed in all primate species versus mouse and rat (left gragh). The global pattern conformed to the three across the nine species and their phylogenetic distance (right graph)

Fig. 3

Whole-genome trinucleotide STR abundance in the nine selected species. While global decremented patterns were observed in primates versus rodents (left graph), human stood out in this category, in comparison to all other species (right graph)

Fig. 4

Example of STRs and STR lengths, abundance of which coincided with the phylogeny of the nine selected species. Three STRs are depicted as examples for each of mono, di, and trinucleotide categories. Data from all studied STRs are available at: https://figshare.com/articles/figure/STR_Clustering/17054972

Fig. 5

Example of STRs and STR lengths, abundance of which appeared to be predominantly random across the nine selected species. Three STRs are depicted as examples for each of mono, di, and trinucleotide categories. Data from all studied STRs are available at: https://figshare.com/articles/figure/STR_Clustering/17054972

Fig. 6

Potential recruitment of qualitatively and quantitatively different TFs to various lengths of (T)-repeats. (T)10 (A) and (T)12 (B) conformed to the phylogenetic < clusters>, whereas (T)14 (C) did not. Differential recruitment of TFs may differentially regulate the relevant genes in evolutionary processes

Fig. 7

Potential differential TF recruitments to various lengths of (ct)6 A) and (ct)7 B). Those two lengths result in alternative quantitative binding of three TFs. (ct)6 conformed and (ct)7 did not conform to the phylogenetic < clusters>