Relative positions and conservation of the CR_holarctica segments in the genomes of Francisella strains. (A) The relative positioning of the CR_holarctica mapped onto the SCHU S4 genome sequence. The outer scale designates coordinates of the whole-genome sequence in base pairs. The outer circle shows predicted coding regions on the plus strand color coded by role categories: violet, amino acid biosynthesis; light blue, biosynthesis of cofactors, prosthetic groups, and carriers; light green, cell envelope; red, cellular processes; brown, central intermediary metabolism; yellow, DNA metabolism; light gray, energy metabolism; magenta, fatty acid and phospholipid metabolism; pink, protein synthesis and fate; orange, purines, pyrimidines, nucleosides, and nucleotides; olive, regulatory functions and signal transduction; dark green, transcription; teal, transport and binding proteins; gray, unknown function; salmon, other categories; blue, hypothetical proteins. The second circle shows the location of all copies of ISftu1 (gray) and ISftu2 (blue) elements in the SCHU S4 genome. The fourth (innermost) circle shows the genomic location of the CR_holarctica in the SCHU S4 genome sequence immediately above the corresponding CR number. The third circle shows the color-coded matching location of the CR_holarctica in the LVS genome. (B) The conservation of CR_holarctica within geographically and temporally distinct sets of Francisella strains. The outer scale designates coordinates in base pairs. The first circle shows predicted coding regions on the plus strand color coded by role categories: violet, amino acid biosynthesis; light blue, biosynthesis of cofactors, prosthetic groups, and carriers; light green, cell envelope; red, cellular processes; brown, central intermediary metabolism; yellow, DNA metabolism; light gray, energy metabolism; magenta, fatty acid and phospholipid metabolism; pink, protein synthesis and fate; orange, purines, pyrimidines, nucleosides, and nucleotides; olive, regulatory functions and signal transduction; dark green, transcription; teal, transport and binding proteins; gray, unknown function; salmon, other categories; blue, hypothetical proteins. The third circle depicts the genomic location of the 17 F. tularensis CR_holarctica as indicated by their CR_holarctica number. The second circle represents the color-coded matching location of each of the 17 F. tularensisCR_holarctica distributed onto the genome of F. tularensis SCHU S4. The remaining circles display the CG-PCR results for each of the 17 loci for a panel of Francisella strains. The circles shaded in pink represent the following four strains (from the outer to inner layer): F. tularensis subsp. holarctica-japan and F. tularensis subsp. novicida strains 15482, Tu-43, and D2005067002. The circles shaded in light yellow represent the following 20 type A strains: Tu-30, SchuS4, NE-UNMC061598, NE-UNL091902, OK-00101504, OK-98041035, NC-54558-01, NC-52797-99, NC-54559-01, CDC NE 031457, UNL 072704, ATCC 6223, A88R160, 88R52, 88R144, AK-1133496, AK-1100558, AK1100559, WY-00W4114, and WY-WSVL02. The circles shaded in yellow represent the following 19 type B strains: LVS, Tu-28, Tu-29, Tu-35, Tu-42, Tu-1, Tu-2, Tu-3, Tu-4, Tu-5, Tu-6, Tu-7, Tu-8, Tu-9, Tu-10, Tu-11, Tu-12, Tu-13, and Tu-14. An additional 48 type B strains were tested that gave results identical to LVS. A negative PCR result is indicated by the absence of the CR box, and light and dark gray CR boxes correspond to PCR unique (not predicted for either SCHU S4 or LVS) for each given locus. Note that geographic locations as well as other demographic information for the strains may be obtained from Table S1 in the supplemental material.

CR13 aligned onto the circular SCHU S4 map. The top line of genes indicates the organization of the contiguous CR13 segment in the LVS genome with the coordinates of the CR indicated above. The locus tags from the SCHU S4 genome sequence are indicated below the genes, with those designated by a prefix or suffix “T” indicating genes truncated due to the beginning or ending of the cloned contig or due to altered arrangements of genomic structure within SCHU S4 compared to LVS. The relative positioning of the genes in the SCHU S4 genome is represented by rectangles on the circle and the corresponding color-coded locations in the LVS genome sequence indicated in the inner ring of the circle. Locus tag annotation is indicated to the right and left of the circle.

Saturation of the PESM library. The cumulative number of contigs is plotted on the y axis as a function of the number of paired-end reads from the PESM library.

Juxtapositioning of CR_holarctica segments in the F. tularensis subsp. tularensis SCHU S4 genome sequence. Shown are the CR_holarctica segments from CR1 and CR16, CR4 and CR10, and CR13 and CR15 in their relative organizations in the SCHU S4 genome sequence and the LVS genome sequence. (A) CR1-CR16; (B) CR4-CR10; (C) CR13-CR15. Corresponding genes from the SCHU S4 and LVS genome sequence are indicated by the same color with the locus tag identifier number listed below the genes. The relative positioning and organization of corresponding genes between the two genomes is highlighted by the peach coloring, with inversions reflected by the hourglass shape of the coloring. (C) Putative orthologues of glpK (glycerol kinase), glpF (glycerol uptake facilitator), and glpA (glycerol-3-phosphate dehydrogenase) are indicated above or below the corresponding gene.