Figure 3

ESOM of genomic sequence fragments based on tetranucleotide frequency (5-kb window size; all contigs > 2 kb were considered). Note that the map is continuous from top to bottom and side to side. (a) Each point represents a sequence fragment; sequences whose origin is known (from assembly information) are colored as indicated below. Unassigned sequences are shown in green. Regions are numbered as follows: (1) ARMAN-2, brown; (2) Ferroplasma (F. acidarmanus fer1, dark orange; fer1(env), orange; fer2(env), light orange); (3) I-plasma, purple; (4) Leptospirillum group II, light blue; (5) Leptospirillum group III, pink; (6) A-plasma, navy blue; (7) E-plasma, light purple; (8) G-plasma, turquoise; (9) ARMAN-4, black; (10) ARMAN-5, red. Regions 11 to 17 are novel genomic regions identified in this study: (11) putative Leptospirillum plasmid; (12) A-plasma variant and C-plasma; (13) D-plasma; (14) Leptospirillum group III variant; (15) an actinobacterium; (16) mixed Actinobacteria; (17) mixed low-abundance bacteria, including Sulfobacillus spp., other Firmicutes, and a gammaproteobacterium. (b) Topography (U-Matrix) representing the structure of the underlying tetranucleotide frequency data from (a). 'Elevation' represents the difference in tetranucleotide frequency profile between nodes of the ESOM matrix (see legend); high 'elevations' (brown, white) indicate large differences in tetranucleotide frequency and thus represent natural divisions between taxonomic groups.