Figure 1.

Genes with different phylogenetic affinities in a ribosomal operon from Aquifex aeolicus and Rickettsia prowazekii. (a) A fragment of ribosomal operon in Aquifex aeolicus (the operon from Thermotoga maritima is shown for comparison), Rickettsia prowazekii and Rickettsia conorrii (operons from other alpha-proteobacteria are shown for comparison). Genes are shown not to scale; the direction of transcription is indicated by arrows and gene numbers/names are given inside each arrow. Orthologous genes are shown by the same color. White arrows show genes in each genome that are unique in this operonic context. Phylogenetic affinity of a gene is shown as a thick colored border on the respective arrow; black denotes belonging to the reference taxon, red denotes not belonging to reference taxon. COG0197 - ribosomal protein L16/L10E; COG0255 - ribosomal protein L29; COG0186 - ribosomal protein S17. For species abbreviations, see Materials and methods. (b) Unrooted maximum-likelihood tree for ribosomal protein L16. Branches supported by bootstrap probability >70% are marked by black circles. Names of the genes from mosaic operons and the respective branches are shown in red. Branches for which the likelihoods of alternative placements were assessed using the RELL method are indicated by circles with numbers (see Table 3). (c) Unrooted maximum-likelihood tree for ribosomal protein L29;. the designations are as in Figure 1b. (d) Unrooted maximum-likelihood tree for ribosomal protein S17; the designations are as in Figure 1b.