The genome and variation of Bacillus anthracis

Abstract

The Bacillus anthracis genome reflects its close genetic ties to Bacillus cereus and Bacillus thuringiensis but has been shaped by its own unique biology and evolutionary forces. The genome is comprised of a chromosome and two large virulence plasmids, pXO1 and pXO2. The chromosome is mostly co-linear among B. anthracis strains and even with the closest near neighbor strains. An exception to this pattern has been observed in a large inversion in an attenuated strain suggesting that chromosome co-linearity is important to the natural biology of this pathogen. In general, there are few polymorphic nucleotides among B. anthracis strains reflecting the short evolutionary time since its derivation from a B. cereus-like ancestor. The exceptions to this lack of diversity are the variable number tandem repeat (VNTR) loci that exist in genic and non genic regions of the chromosome and both plasmids. Their variation is associated with high mutability that is driven by rapid insertion and deletion of the repeats within an array. A notable example is found in the vrrC locus which is homologous to known DNA translocase genes from other bacteria.

Figure 1

Phylogenetic structure of B. anthracis.

Figure 2

Alignments of four whole chromosomes. The Artemis software (Rutherford et al., 2000) was used to analyze four closed genomes. This figure is a series of lines connecting pairwise regions of each genome. The red lines indicate sequence similarity between directly repeated regions while the blue lines are indicative of sequence similarity in a reverse orientation. White regions are indels, indicating the presence/absence of a particular region between the genome pairs.

Figure 3

“Icicle” plot of tandemly repeated sequences. This is a graphical representation of the tandemly repeated loci in the Ames genome. The longer “icicles” are indicative of longer tandem arrays at those loci.

Figure 4

A dotplot homology analysis of the vrrC locus. The VNTR region of the vrrC gene was analyzed using a dot plot algorithm, which compares a particular sequence against itself. The diagonal lines are indicative of directly repeated DNA sequences in this region of the genome. The strong diagonal line in the middle is the identity line and each half of the box contains the same information, in a mirrored fashion. Note that there are three separate tandemly repeated subregions, termed vrrC₁, vrrC₂, and vrrC₃. The strong diagonal lines near the identity line, show the level of identity between direct repeats and the spacing also is indicative or the repeat length. Each subregion is compared to the others in a pair-wise fashion as indicated: a) vrrC₁ × vrrC₂; b) vrrC₁ × vrrC₃; and c) vrrC₂ × vrrC₃.