Comparative Analysis of Predicted SSR Sequences and CpG Islands to Discover Evolutionary Relics of Sex-chromosomes in Divergent Animal Species

Abstract

Background: DNA markers have high occurrence and mutation rates and are generally located around the controlling regions of some tissue-specific genes and housekeeping genes that can change the expression pattern. Microsatellites and CpG islands are stretches of DNA with repeats and are known to influence gene expression. Methods: In the present study, these DNA markers are mined and an In silico comparison was carried out to understand their occurrence pattern and distribution frequency in sex chromosomes (X and Y) of 12 different animal species using Perl and R programming pipelines. Result: It was found that female-dominant X chromosomes had higher occurrence and distribution frequencies for these DNA markers than that of male-dominant sex chromosome i.e. Y which means that the former has a higher number of the evolutionary sites.The density of DNA markers however, showed remarkable variation for different animal species. The results obtained need validation through wet-lab experimentation. Tri- and hexa-nucleotide repeats are more abundant in exons, whereas other repeats are more abundant in non-coding regions.