Circular representation of the S. pneumoniae TIGR4 genome and comparative genome hybridizations using microarrays. Comparative genome hybridizations are used to identify genomic differences between the TIGR4 isolate and strains R6 and D39, using a preliminary microarray. Results are displayed on the third and fourth circles. Genes were classified in four groups: (i) gene not present on the array and not analyzed (black) (394 genes, 17% of total); (ii) ortholog present in the test strain (green); (iii) ortholog absent in the test strain (red); and (iv) ambiguous result (blue). The Cy3/Cy5 ratio (TIGR4 signal/test strain) cutoffs for each category were determined subjectively as Cy3/Cy5 5 1.0 to 3.0, green; 3.0 to 10.0, blue; and >10.0, red. There were a number of loci for which hybridization ratios fell between what is expected for gene presence or absence (Cy3/Cy5ratios between 3.0 to 10.0). Ambiguous results (blue bars) can be explained in at least two ways: (i) The gene may be highly diverged inR6 and/or D39 relative to the TIGR4 isolate. (ii) Alternatively, the gene may be absent in R6 and/or D39 but still be able to produce a hybridization signal, because the TIGR4 isolate gene is a member of a paralogous gene family or a repetitive element. The outer circle shows predicted coding regions on the plus strand, color-coded by role categories: salmon, amino acid biosynthesis; light blue, biosynthesis of cofactors and prosthetic groups and carriers; light green, cell envelope; red, cellular processes; brown, central intermediary metabolism; yellow, DNA metabolism; green, energy metabolism; purple, fatty acid and phospholipid metabolism; pink, protein fate/synthesis; orange, purines, pyrimidines, nucleosides, and nucleotides; blue, regulatory functions; grey, transcription; teal, transport and binding proteins; black, hypothetical and conserved hypothetical proteins. The second circle shows predicted coding regions on the minus strand, color-coded by role categories. The third circle shows strain R6genes. The fourth circle shows strain D39 genes. The fifth circle shows an atypical nucleotide composition curve; the nine gene clusters that are absent in strains R6 and D39 are indicated by red bullets. The sixth circle shows the GC-skew curve. The seventh circle shows IS elements. The eighth circle shows RUP elements. The ninth circle shows BOX elements. The tenth circle shows rRNAs in blue, tRNAs in green, and structural RNAs in red.

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