Visualization of ribosomal RNA operon copy number distribution

A representative Bacterial tree was constructed using 31 marker genes found in 578 bacterial genome sequences. Organism names are displayed on the trees using graduations of color such that similar colors indicate similar numbers of operons or genome size. The resulting images provide an intuitive understanding of how copy number and genome size vary in different Bacterial phyla.Once the phylogenetic position of a novel organism is known the number of rRNA operons, and to a lesser extent the genome size, can be estimated by examination of the colored maps. Further detail can then be obtained for members of relevant taxa from the rrnDB database.The ribosomal RNA (rRNA) genes of Bacteria and Archaea are typically found in operons. Although many organisms have a single rRNA operon the actual number is known to vary between 1 and 15 [1]. The operons themselves do not always exhibit the same sequence but instead different in a modest number of positions, typically less than 15 in the case of 16S rRNAs. Nevertheless, there are exceptions. For example, one of the three 16S rRNA genes in Halobacterium marismortui differs from the others in over 70 positions [2]. Such microheterogeneity has been studied in detail in a modest number of cases. For example, it has been recently shown is in Streptomyces coelicolor that all the operons are expressed and their RNAs incorporated into ribosomes but the relative expression level may vary over the growth cycle [3,4]. In the case of H. marismortui, the aberrant operon responds to temperature differently [5]. Efforts to evaluate the extent of rRNA operon microheterogeneity likely should be handled cautiously. An examination of complete genome sequences revealed many examples where all the 16S rRNA genes in an organism with multiple rRNA operons are reported to be identical [6]. There certainly are cases where multiple rRNAs exist with the same sequence. However, in the case of the rapidly accumulating bacterial genomes, one must remembe