Insertion sequence elements-mediated structural variations in bacterial genomes

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.

Keywords: Bacterial genomes; Insertion sequence elements; Mutation accumulation; Structural variations.

Fig. 1

IS insertion rates vary across different bacterial genomes. IS insertion rates of various bacterial genomes are compared to the IS insertion rates in the wild-type and 12 DNA repair deficient mutants of E. coli K12 MG1655 reported previously [21]. This figure plotted the number of observed IS insertions (y-axis) versus the total number of generations (x-axis) in a group of MA lines originating from the same founder strain in a single experiment. While all the MA experiments on E. coli K12 MG1655 exhibited a linear relationship between the number of insertions and the number of generations, suggesting a constant IS insertion rate per generation across these lines, only in some of the other E. coli strains and bacterial species studied here, similar IS insertion rates were observed. In contrast, much higher rates were observed in wild-type D. radiodurans BAA-816 and E. coli REL4536 grown in the anaerobical condition, whereas much lower rates are observed in E. coli ED1a and IAI1 strains.For the linear regression, the dotted line shows the 95% confidence interval boundaries