Figure 5

Genomotyping and similarity analysis between the genomes of XAC and XauC based on DNA hybridization and matching of contig sequences. (A) The hybridization results showed that 2,486 CDSs (out of a total 2,760) gave a hybridization signal greater than the estimated background noise. Of the 2,486 CDSs, 2,341 (94.2%) seem to be present in XauC (ratio Cy3/Cy5 between 0 and 1.5). The remaining 145 CDSs (5.8%) seem specific to XAC. (B) Of these 145, most (101 = 70%) belong to regions previously described as putative genomic islands in XAC (black ovals: [14]; green ovals: [106]; yellow ovals: [31]; the oval numbering corresponds to the original publication numbering). Pink ovals mark other nonsimilar regions between the genomes of XAC and XauC. (C) The two bottommost graphs (G+C and codon bias) show variation of these two metrics along the XAC genome, thus presenting evidence for the putative genomic islands denoted by ovals. The numbered triangles correspond to the XAC-specific regions based on DNA hybridization. Blue horizontal bars simply denote regions in these graphs that correspond to ovals not associated with XAC-specific regions. The Heat Map shows gene groups that yielded differential hybridization signals, the vast majority of which correspond to regions marked by ovals. The zoomed-in regions in the upper diagram show genes with differential hybridization signals but that are in regions shared by the two genomes. The XAC and XauC genes in these regions have less similarity (from 42 to 68% identity) between them than other shared genes.