In addition, in some instances the number Ruxolitinib order of copies of each rRNA is different. This is most frequent for 5S rRNA, which may be present in an extra copy. In these cases, the number of 16S rRNA genes was used as the number of operons as in most practical applications it is 16S rRNA that is being examined. The tree was combined with the operon and information and built using Newick format such that each node is specified http://en.wikipedia.org/wiki/Newick by “”species-name*genome-size*rRNA-operon-count”". The organism names on the tree were colored
according to either operon number or genome size. In each case, as the parameter increases the color generally becomes darker. Thus, for the operons 14 colors were used. For 0 to 6 operons, shades of yellow, orange or red were used with darker colors indicating larger numbers of operons. For 7 to 10 operons shades of blue were used and greens were used for 11 or more. In the case of genome size, 12 colors were used to depict various size ranges. The first
range was 0-1 MB with subsequent increments of 0.5 MB. The final range was for genomes greater than 6 MB in size. The final tree was created in the .esp format using ATV . Results Bacterial rRNA operon copy number was mapped onto a phylogenetic tree by coloring the organism names on each branch in accordance with the number of operons (Figure 1 and Additional selleck products file 1). Genome size was separately mapped in a similar manner (Figure 2 and Additional file 2). These maps allow one to readily Ketotifen visualize the extent to which these properties have been conserved over phylogenetic
distance. In both cases, the values are conserved within species and frequently within genera as well. In the case of operon number, similar values are frequently found in neighboring groupings as well. Overall, rRNA operon number typically only exceeds six in two regions of the tree, the γ-Proteobacteria and the Firmicutes, e.g. Bacillus, Staphylococcus, Streptococcus, and others . Thus, if one knows the approximate phylogenetic position of an organism one can make a reasonable prediction of how many rRNA operons it will have. As previously noted, genome size and operon number are largely uncorrelated with the one exception that organisms with genome sizes below 1.5 MB almost never have more than one rRNA operon. Figure 1 Phylogenetic tree colored according to operon copy number. Each organism name on the tree is followed by the approximate size of its genome in megabases, (MB), and the number of rRNA operons found in the genome. The color of the lettering is decided by the number of operons. Fourteen distinct colors were used with each assigned to a specific number of operons. As the operon number increases the color used generally becomes darker. The darkish shade of green is used for 13 or more copies. This figure shows the upper quartile, for the full image please see Additional file 1. Figure 2 Phylogenetic tree colored according to genome size.