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Haloquadratum walsbyi : Limited Diversity in a Global Pond

Figure 5

Comparison of the chromosomes of Hqr. walsbyi strains C23T and HBSQ001.

Panel A: Mummer nucleotide alignment, where dots indicate similar sequences in the same orientation (red), or reverse orientation (blue), shared by the two strains. Panels B and D: Tetra-nucleotide variation (TETRA) along the chromosomal sequences of each strain (labeled). Several divergent regions in each plot are labeled in both panels (see text). The %G+C deviation (if a 1 kb window is more than 2.5 SD from the average) is given for HBSQ001 immediately below the panel TETRA plot of panel D. Panel C: comparison of the chromosomal sequences using the Artemis comparison tool (ACT). Red lines indicate regions of high nucleotide similarity; white regions indicate lack of similarity. Above this plot regions of major divergence (DV 1-12) are indicated (and also on the Mummer plot in panel A), while below the previously described genomic islands (GI 1-4 [13]) are indicated. Panel E: Cumulative GC-skew plots for the chromosomes of C23T (red) and HBSQ001 (black). The boxed region extending upwards to panel D outlines the major drop in the cumulative skew plot of HBSQ001.

Figure 5

doi: https://doi.org/10.1371/journal.pone.0020968.g005