Figure 2

Whole-genome proteome alignments. Plots show the chromosome locations of pairs of predicted proteins that have significant similarity (on the basis of fasta3 comparisons). (a) V. cholerae chrI versus E. coli. All significant matches for each V. cholerae ORF are shown. (b) V. cholerae chrI versus E. coli, top matches. Only the best match for each V. cholerae ORF is shown. The filtering for top matches for each ORF removes noise due to the presence of many large multigene families. This X-alignment is highly statistically significant (Table 2). (c) Chlamydia trachomatis versus C. pneumoniae, top matches. Only the best match for each C. trachomatis ORF is shown. The position of the origins (R) and termini (T) of replication are slightly shifted to see the inversions better. This pattern is consistent with the occurrence a small number of inversions around the origin and terminus in the two lineages since their divergence from a common ancestor (see Figure 4). (d) V. cholerae chrI versus V. cholerae chrI, self-alignment. Only recently duplicated pairs of genes are shown. Recent duplications were operationally defined as those genes that were more similar to another gene in V. cholerae than to any gene in any other complete genome sequence. The faint X-alignment is statistically significant (Table 2). No significant X-alignment was detected when all pairs of paralogs were included.