Rearrangement analysis of multiple bacterial genomes

Mehwish Noureen,Ipputa Tada,Takeshi Kawashima,Masanori Arita

doi:10.1186/s12859-019-3293-4

Abstract

BackgroundGenomes are subjected to rearrangements that change the orientation and ordering of genes during evolution. The most common rearrangements that occur in uni-chromosomal genomes are inversions (or reversals) to adapt to the changing environment. Since genome rearrangements are rarer than point mutations, gene order with sequence data can facilitate more robust phylogenetic reconstruction. Helicobacter pylori is a good model because of its unique evolution in niche environment.ResultsWe have developed a method to identify genome rearrangements by comparing almost-conserved genes among closely related strains. Orthologous gene clusters, rather than the gene sequences, are used to align the gene order so that comparison of large number of genomes becomes easier. Comparison of 72 Helicobacter pylori strains revealed shared as well as strain-specific reversals, some of which were found in different geographical locations.ConclusionDegree of genome rearrangements increases with time. Therefore, gene orders can be used to study the evolutionary relationship among species and strains. Multiple genome comparison helps to identify the strain-specific as well as shared reversals. Identification of the time course of rearrangements can provide insights into evolutionary events.

Highlights

Genomes are subjected to rearrangements that change the orientation and ordering of genes during evolution
Degree of genome rearrangements increases with time as point mutations accumulate, both reflecting the evolutionary history of genomes
Gene orders can be used as a measure to study the evolutionary relationship of species

Summary

Introduction

Genomes are subjected to rearrangements that change the orientation and ordering of genes during evolution. The most common rearrangements that occur in uni-chromosomal genomes are inversions (or reversals) to adapt to the changing environment. Since genome rearrangements are rarer than point mutations, gene order with sequence data can facilitate more robust phylogenetic reconstruction. Helicobacter pylori is a good model because of its unique evolution in niche environment. Each species has a specific genome structure that changes slowly with time. In DNA sequences, local and global mutations occur. Local mutations include substitution (point mutation), insertion and deletion of a single nucleotide [1]. Global mutations (genome rearrangements) include inversion ( known as reversal), translocation, duplication, and transposition [2].

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