title: Genetic variation and linkage disequilibrium in Bacillus anthracis.
abstract: We performed whole-genome amplification followed by hybridization of custom-designed resequencing arrays to resequence 303 kb of genomic sequence from a worldwide panel of 39 Bacillus anthracis strains. We used an efficient algorithm contained within a custom software program, UniqueMER, to identify and mask repetitive sequences on the resequencing array to reduce false-positive identification of genetic variation, which can arise from cross-hybridization. We discovered a total of 240 single nucleotide variants (SNVs) and showed that B. anthracis strains have an average of 2.25 differences per 10,000 bases in the region we resequenced. Common SNVs in this region are found to be in complete linkage disequilibrium. These patterns of variation suggest there has been little if any historical recombination among B. anthracis strains since the origin of the pathogen. This pattern of common genetic variation suggests a framework for recognizing new or genetically engineered strains.
authors.affiliation: Biological Defense Research Directorate, Naval Medical Research Center, Silver Spring, MD, USA. mzwick@emory.edu
authors.forename: Michael E
authors.initials: ME
authors.lastname: Zwick
authors.forename: Maureen Kiley
authors.initials: MK
authors.lastname: Thomason
authors.forename: Peter E
authors.initials: PE
authors.lastname: Chen
authors.forename: Henry R
authors.initials: HR
authors.lastname: Johnson
authors.forename: Shanmuga
authors.initials: S
authors.lastname: Sozhamannan
authors.forename: Alfred
authors.initials: A
authors.lastname: Mateczun
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Read
mesh_terms: D000483:Alleles; D000818:Animals; D001408:Bacillus anthracis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D015373:Bacterial Typing Techniques; D004269:DNA, Bacterial / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D015810:Linkage Disequilibrium; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic
chemical_list: D004269:DNA, Bacterial