SSR repeat dynamics in mitochondrial genomes of five domestic animal species.

Sushil Kumar Shakyawar,Dinesh Kumar,Balwindar Kumar Joshi

doi:10.6026/97320630004158

Abstract

SSR (simple sequence repeats) are ubiquitously abundant in genomes. In organellar mitochondrial genome of animals, its distribution, size dynamics and effectiveness for phylogenetic relationship have not been understood. Present investigation reveals organisation of SSR in genic and intergenic region, its length and repeat motif dynamics, extent of conservation of flanking regions, appropriateness of these SSR data in establishing phylogenetic relationship. Contrary to eukaryotic nuclear abundance of SSR in non-coding region, we found abundance in coding region. Like nuclear SSR, most hyper mutable repeats were found in non coding region having di nucleotide motifs of mitochondrial genome but contrary to human having high mutable tetra repeats in case of mitochondrial genomes this was found to be with tri-motif repeats. SSR of mitochondrial genomes also show cyclical expansion and shrinkage in pattern of SHM (simple harmonic motion) with respect to time its non- linear thus not appropriate for phylogenetic analysis though the flanking regions of these SSR also conserved like nuclear SSR.

Highlights

The near-absence of genetic recombination and high mutation rate with some selectivity in mitochondrial DNA makes it a useful source for analyzing microsatellite or STR or simple sequence repeat (SSR) dynamics on the archaeological time scale
The relative allelic length difference is calculated from the generated data and is further used to make rooted tree (Figure 2(C) and Discussion: The in silico mining of SSR in mitochondrial genomes of five species reveals that they are more abundant in coding region unlike the nuclear genomes where SSRs are usually present in intronic/non coding regions [9]
simple harmonic motion (SHM) was shown by SSR but not by flanking region of SSR, the cause for this phenomenon is that, the mutation rate of SSRs which is 103/cell/generation that is hyper mutation which is 106 times more

Summary

Introduction

The near-absence of genetic recombination and high mutation rate with some selectivity in mitochondrial DNA makes it a useful source for analyzing microsatellite or STR (simple tandem repeat) or simple sequence repeat (SSR) dynamics on the archaeological time scale. Difference between the mean repeat sizes of two lineages is a linear function of the time since they diverged [1]. Presence of homologous loci in each test of marine species within two families (Cheloniidae and Dermochelyidae), as well as in a freshwater species (Emydidae and Trachemys scripta) is the indication for this constancy approximately over 300 million years of divergent evolution [3].The flanking region is conserved and perpetuates down in evolution but the SSR loci reflects cyclical (shrinkage and expansion) variation in size over time which has been well documented in case of nuclear SSR [4]

Methods

Results

Conclusion