Relatedness of the Thermotoga strains used in this study. (A) Small-subunit rRNA gene phylogeny. *, strains that were compared in the CGH study. (B) CGH results and hierarchical clustering based on the CGH data.

Analysis of the sequenced RQ2 regions compared to their MSB8 counterparts. For each RQ2 region that was sequenced to closure and analyzed, the blue line (top) represents the PCR product obtained for RQ2, whereas the black line (bottom) represents the same region in MSB8. Red lines delimited by two red filled circles were drawn to give length indications of remarkable sequences of the MSB8 genome. The coordinates refer to the start of the PCR product for RQ2 and to the whole genome for MSB8. MSB8 genes (above the black line for MSB8) and RQ2 genes (underneath the blue line for RQ2) are color coded according to their best match. Green, best match to bacterial species; brown, best match to bacterial species; black, hypothetical proteins (no match). The orange line represents the χ² analysis of the G+C content of the MSB8 region (a scale is shown on the right). The brown areas represent the nucleotide identities (values in dark brown) between the MSB8 and RQ2 sequences. Finally, remarkable features are represented, such as predicted “archaeal islands” in the MSB8 genome (brown boxes), repeats (pink boxes).

Circular representation of the T. maritima MSB8 genome and CGHs using microarrays. Outer circle and second circle, predicted coding regions on the plus and the minus strand, respectively, color coded by role categories (10). Third circle, atypical nucleotide composition. Fourth circle, “archaeal islands” as predicted by Nelson et al. (9). Fifth circle, repeats associated with CRISPR elements (red; CRISPR locus numbers from I to VIII are listed), CRISPR-associated sequence loci (half-sized ticks, orange), transposons (blue), and repeat elements (three-quarter-sized ticks, cyan). Sixth circle, CGH regions R1 to R12 (see Tables S1 and S3). The circles 7 to 24 show the CGH results (comparison to MSB8) for strains RQ2 (circles 7 and 8), S1/L12B (circles 9 and 10), PB1platt (circles 11 and 12), NE7/L9B (circles 13 and 14), NE2x/L8B (circles 15 and 16), LA10 (circles 17 and 18), LA4 (circles 19 and 20), RQ7 (circles 21 and 22), and VMA1/L12B (circles 23 and 24). For each strain, the outermost circle represents the hybridization ratio, R (see Materials and Methods); gray, R < 3 (genes shared); yellow, 3 < R < 5; orange, 5 < R < 7; red, 7 < R < 10; brown, R > 10 (genes divergent). The innermost blue circle displays the %EPD for each gene compared to MSB8. The %EPD could not be calculated for strains LA10 (circle 18), LA4 (circle 20), RQ7 (circle 22), and VMA1/L12B (circle 24).