A large scale comparative genomic analysis reveals insertion sites for newly acquired genomic islands in bacterial genomes

Pengcheng Du,Haiying Wang,Chen Chen,Yinxue Yang,Di Liu,George F Gao

doi:10.1186/1471-2180-11-135

Abstract

BackgroundBacterial virulence enhancement and drug resistance are major threats to public health worldwide. Interestingly, newly acquired genomic islands (GIs) from horizontal transfer between different bacteria strains were found in Vibrio cholerae, Streptococcus suis, and Mycobacterium tuberculosis, which caused outbreak of epidemic diseases in recently years.ResultsUsing a large-scale comparative genomic analysis of 1088 complete genomes from all available bacteria (1009) and Archaea (79), we found that newly acquired GIs are often anchored around switch sites of GC-skew (sGCS). After calculating correlations between relative genomic distances of genomic islands to sGCSs and the evolutionary distances of the genomic islands themselves, we found that newly acquired genomic islands are closer to sGCSs than the old ones, indicating that regions around sGCSs are hotspots for genomic island insertion.ConclusionsBased on our results, we believe that genomic regions near sGCSs are hotspots for horizontal transfer of genomic islands, which may significantly affect key properties of epidemic disease-causing pathogens, such as virulence and adaption to new environments.

Highlights

Bacterial virulence enhancement and drug resistance are major threats to public health worldwide
We focus on the strategies for identifying genomic island (GI) and switch sites of GC-skew and propose a new term, putative GI, to denote abnormal G/C loci as GI insertion hotspots in bacterial genomes
Pathogenity Island (PAI), PAI-like sequences overlapping with GIs, and PAI-like sequences not overlapping GIs data were downloaded from the PAI database http://www.gem.re.kr/

Summary

Introduction

Bacterial virulence enhancement and drug resistance are major threats to public health worldwide. It has been found that the directions of GC skew often change at flanking regions around bacterial replication origins [3,4,5,6,7,8]. Strand compositional asymmetry is commonly used to identify locations of bacterial replication origins [3,4,5,6,7]. Strand asymmetry has been widely studied with GC-skew analysis by calculating [GC]/[G+C] in the chromosome or protein coding regions [9,10]., bacterial genomes share many. While mutations generated during replication are an important source of bacterial compositional asymmetry, horizontal acquisition of foreign DNAs, known as genomic islands (GIs), plays an important role. GIs encode many different functions and are thought to have played a major role in the microbial evolution of specific host-recognition, symbiosis, pathogenesis, and virulence [14,15]

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Conclusion