Insertion sequence elements-mediated structural variations in bacterial genomes

Etienne Nzabarushimana,Haixu Tang

doi:10.1186/s13100-018-0134-3

Abstract

Mobile genetic elements (MGEs) impact the evolution and stability of their host genomes. Insertion sequence (IS) elements are the most common MGEs in bacterial genomes and play a crucial role in mediating large-scale variations in bacterial genomes. It is understood that IS elements and MGEs in general coexist in a dynamical equilibrium with their respective hosts. Current studies indicate that the spontaneous movement of IS elements does not follow a constant rate in different bacterial genomes. However, due to the paucity and sparsity of the data, these observations are yet to be conclusive. In this paper, we conducted a comparative analysis of the IS-mediated genome structural variations in ten mutation accumulation (MA) experiments across eight strains of five bacterial species containing IS elements, including four strains of the E. coli. We used GRASPER algorithm, a denovo structural variation (SV) identification algorithm designed to detect SVs involving repetitive sequences in the genome. We observed highly diverse rates of IS insertions and IS-mediated recombinations across different bacterial species as well as across different strains of the same bacterial species. We also observed different rates of the elements from the same IS family in different bacterial genomes, suggesting that the distinction in rates might not be due to the different composition of IS elements across bacterial genomes.

Highlights

The intricacies of mobile genetic elements (MGEs) in their host genomes have challenged if not inspired scientists to understand the evolution and stability of genomes
3.5×10−4 Insertion sequence (IS) insertions and 4.5×10−5 IS-mediated recombinations occur spontaneously per genome per generation in the E. coli K12 MG1655 genome, and these rates remain constant across the wild-type and 12 DNA repair deficient mutants [21]
We conducted a comparative analysis of IS-mediated genome structural variations (SVs) in ten previously published mutation accumulation (MA) experiments [22,23,24,25,26,27] conducted on eight strains from five bacterial species (Table 1, Additional file 1: Table ST1), which span both gram-negative (i.e., E. coli, Burkholderia cenocepacia and Vibrio cholerae) and gram-positive bacteria (i.e., Mycobacterium smegmatis and D. radiodurans)

Summary

Introduction

The intricacies of mobile genetic elements (MGEs) in their host genomes have challenged if not inspired scientists to understand the evolution and stability of genomes. We previously studied the IS-mediated genome structural variations (SVs) in the selection-free conditions using whole genome re-sequencing data from mutation accumulation (MA) lines of the Escherichia coli K12 MG1655 strain [21].

Results

Conclusion