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Open Access Highly Accessed Research article

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

Pengcheng Du1, Yinxue Yang2, Haiying Wang1, Di Liu4, George F Gao35* and Chen Chen1*

Author Affiliations

1 National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, China

2 Affiliated Hospital of Ningxia Medical University, Ningxia 750001, China

3 CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, China

4 Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China

5 Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China

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BMC Microbiology 2011, 11:135  doi:10.1186/1471-2180-11-135

Published: 15 June 2011



Bacterial 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.


Using 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.


Based 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.

switch sites of GC-skew; genomic island; evolution