Schematic circular diagrams of the B. cenocepacia J2315 genome. The circular diagrams for chromosomes 1 (A) and 2 (B) are drawn to scale, whereas those for chromosome 3 (C) and plasmid pBCJ2315 (D) are not drawn to scale. Black circles representing these replicons are drawn to scale. The key for the three chromosomal circular diagrams (A, B, and C; outside to inside), with scale in Mb, is as follows. Annotated CDSs are colored according to the predicted function represented on a pair of concentric circles, representing both coding strands. CDSs in genomic island regions are indicated in green, and other RODs defined by pairwise genome comparisons with other BCC are indicated in red. CDSs with matches identified by reciprocal FASTA with other Burkholderia species—B. cenocepacia HI2424, B. cenocepacia AU1054, B. contaminans 383, B. ambifaria AMMD, B. vietnamiensis G4, B. xenovorans LB400, B. pseudomallei K96243, and B. thailandensis E264—are indicated in dark blue. Orthologues shared with Ralstonia solanacearum GMI1000 are indicated in purple. For the G+C content plot, the GC bias (G−C/G+C) is indicated as >1% in khaki and <1% in purple. (D) The key for the circular diagram for plasmid pBCJ2315 is as described for the chromosomes but lacks the orthologue matches. Color coding for CDS functions: dark blue for pathogenicity/adaptation, black for energy metabolism, red for information transfer, dark green for surface associated, cyan for degradation of large molecules, magenta for degradation of small molecules, yellow for central/intermediary metabolism, pale green for unknown, pale blue for regulators, orange for conserved hypothetical, brown for pseudogenes, pink for phage and IS elements, and gray for miscellaneous.