Genetic Markers of Genome Rearrangements in Helicobacter pylori

Abstract

Helicobacter pylori exhibits a diverse genomic structure with high mutation and recombination rates. Various genetic elements function as drivers of this genomic diversity including genome rearrangements. Identifying the association of these elements with rearrangements can pave the way to understand its genome evolution. We analyzed the order of orthologous genes among 72 publicly available complete genomes to identify large genome rearrangements, and rearrangement breakpoints were compared with the positions of insertion sequences, genomic islands, and restriction modification genes. Comparison of the shared inversions revealed the conserved genomic elements across strains from different geographical locations. Some were region-specific and others were global, indicating that highly shared rearrangements and their markers were more ancestral than strain-or region-specific ones. The locations of genomic islands were an important factor for the occurrence of the rearrangements. Comparative genomics helps to evaluate the conservation of various elements contributing to the diversity across genomes.

Keywords: Helicobacter pylori; insertion sequences; inversion breakpoints; repeats.

Figure 1

(a) Graphical representation of the Helicobacter pylori 26695 strain. Four breakpoints are indicated by crossing lines and the corresponding labels represent the breakpoint number (B1–B4). Two genomic islands (GIs) were identified in this strain that are present at the location of two breakpoints B3 and B4. Within these GIs, IS605 was present as an inverted repeat. (b) Graphical representation of H. pylori Aklavik117 strain. This strain possessed the two GIs almost at the same location as in (a), but it lacked the insertion sequence (IS) elements in these GIs and the inversion R2 was absent.

Figure 2

Distribution of shared breakpoints among strains from different geographical locations. Breakpoints are designated as B1–B30. B22–B27 can be regarded as East-Asia-specific.

Figure 3

Distribution of direct and inverted repeats in different geographical regions. Region names are abbreviated (AF: Africa, AU: Australia, EA: East Asia, EU: Europe, IN: India, SA: South America, UN: region not known, and NA: North America). Red dots represent the average number of repeats identified in each region. Regions with the largest number of repeats on average are encircled.

Figure 4

Presence of different elements around shared breakpoints at the strain level. Each column represents one strain (names indicated at the bottom) whereas each row indicates one shared breakpoint. Colored bars below strain names indicate the different regions (Yellow: East Asia, Red: South America, Purple: North America, Green: Europe, Brown: Africa, Black: Region not known, Blue: India, and Grey: Australia). Different colors in the cells represent different elements. The while cells indicate the absence of breakpoint.