title: Conservation in the face of diversity: multistrain analysis of an intracellular bacterium.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Program in Genomics, Department of Veterinary Microbiology and Pathology, School for Global Animal Health, Washington State University, Pullman, WA 99164-7040, USA. darkmich@wsu.edu
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Dark
authors.forename: David R
authors.initials: DR
authors.lastname: Herndon
authors.forename: Lowell S
authors.initials: LS
authors.lastname: Kappmeyer
authors.forename: Mikel P
authors.initials: MP
authors.lastname: Gonzales
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Nordeen
authors.forename: Guy H
authors.initials: GH
authors.lastname: Palmer
authors.forename: Donald P
authors.initials: DP
authors.lastname: Knowles
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Brayton
mesh_terms: D042322:Anaplasma marginale / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial; D017124:Conserved Sequence; D004269:DNA, Bacterial / Q000235:genetics; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D015698:Genomic Library; D016366:Open Reading Frames; D010641:Phenotype; D020161:Physical Chromosome Mapping; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D004269:DNA, Bacterial