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Open Access Research article

Conservation in the face of diversity: multistrain analysis of an intracellular bacterium

Michael J Dark1, David R Herndon2, Lowell S Kappmeyer2, Mikel P Gonzales3, Elizabeth Nordeen1, Guy H Palmer1, Donald P Knowles12 and Kelly A Brayton1*

Author Affiliations

1 Program in Genomics, Department of Veterinary Microbiology and Pathology, School for Global Animal Health, Washington State University, Pullman, WA 99164-7040, USA

2 Animal Disease Research Unit, U.S. Department of Agriculture/Agriculture Research Service, Pullman, WA 99164-7030, USA

3 College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766-1854, USA

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BMC Genomics 2009, 10:16  doi:10.1186/1471-2164-10-16

Published: 11 January 2009

Abstract

Background

With the recent completion of numerous sequenced bacterial genomes, notable advances have been made in understanding the level of conservation between various species. However, relatively little is known about the genomic diversity among strains. We determined the complete genome sequence of the Florida strain of Anaplasma marginale, and near complete (>96%) sequences for an additional three strains, for comparative analysis with the previously fully sequenced St. Maries strain genome.

Results

These comparisons revealed that A. marginale has a closed-core genome with few highly plastic regions, which include the msp2 and msp3 genes, as well as the aaap locus. Comparison of the Florida and St. Maries genome sequences found that SNPs comprise 0.8% of the longer Florida genome, with 33.5% of the total SNPs between all five strains present in at least two strains and 3.0% of SNPs present in all strains except Florida. Comparison of genomes from three strains of Mycobacterium tuberculosis, Bacillus anthracis, and Nessieria meningiditis, as well as four Chlamydophila pneumoniae strains found that 98.8%–100% of SNPs are unique to each strain, suggesting A. marginale, with 76.0%, has an intermediate level of strain-specific SNPs. Comparison of genomes from other organisms revealed variation in diversity that did not segregate with the environmental niche the bacterium occupies, ranging from 0.00% to 8.00% of the larger pairwise-compared genome.

Conclusion

Analysis of multiple A. marginale strains suggests intracellular bacteria have more variable SNP retention rates than previously reported, and may have closed-core genomes in response to the host organism environment and/or reductive evolution.