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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 16.
Published online Jan 11, 2009. doi:  10.1186/1471-2164-10-16
PMCID: PMC2649000
Conservation in the face of diversity: multistrain analysis of an intracellular bacterium
Michael J Dark,1 David R Herndon,2 Lowell S Kappmeyer,2 Mikel P Gonzales,3 Elizabeth Nordeen,1 Guy H Palmer,1 Donald P Knowles, Jr,1,2 and Kelly A Braytoncorresponding author1
1Program in Genomics, Department of Veterinary Microbiology and Pathology, School for Global Animal Health, Washington State University, Pullman, WA 99164-7040, USA
2Animal Disease Research Unit, U.S. Department of Agriculture/Agriculture Research Service, Pullman, WA 99164-7030, USA
3College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766-1854, USA
corresponding authorCorresponding author.
Michael J Dark: darkmich/at/wsu.edu; David R Herndon: herndon/at/vetmed.wsu.edu; Lowell S Kappmeyer: lkapp/at/vetmed.wsu.edu; Mikel P Gonzales: mgonzales/at/westernu.edu; Elizabeth Nordeen: enordeen/at/vetmed.wsu.edu; Guy H Palmer: gpalmer/at/vetmed.wsu.edu; Donald P Knowles, Jr: dknowles/at/vetmed.wsu.edu; Kelly A Brayton: kbrayton/at/vetmed.wsu.edu
Received July 3, 2008; Accepted January 11, 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.
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