Distribution and evolution of simple repeats in the mtDNA D-loop in mammalian

Abstract

Simple sequence repeats (SSR) distribute extensively in genomes of all organisms, but the molecular mechanism underlined is poorly understood. In this study, we characterized distribution and biological significance of the simple repetitive DNA sequences in the D-loop region in mitochondria DNA of 256 mammal species, and classified the mammal carriers into three groups including 53 species with hexanucleotide repeats, 104 species with other types of simple repeats (>6 bp) and 99 species without any repeat sequences, respectively. Furthermore, we found that the hexanucleotide repeats dispersed significantly in the interval space between CSB1 and CSB2, while other repeats dispersed mainly in the termination region, central conserved region and the conserve sequence block (CSB) regions. In addition, comparison on the base composition and the DNA contexts of the central conserved region, CSB1, CSB2, and CSB3 revealed a lack of significant differences in similarity among different species with or without repeat sequences. Moreover, a phylogenetic analysis with 256 mammal species using N-J method suggested loss of the repeat sequences in mammals in evolution.