Visualization of ribosomal RNA operon copy number distribution
1 Dept of Computer Science, University of Houston, Houston, Texas, USA
2 Dept of Biology, University of Virginia, Charlottesville, Virginia, USA
3 Dept of Biology and Biochemistry, University of Houston, Houston, Texas, USA
BMC Microbiology 2009, 9:208 doi:10.1186/1471-2180-9-208Published: 25 September 2009
Results of microbial ecology studies using 16S rRNA sequence information can be deceiving due to differences in rRNA operon copy number and genome size of the detected organisms. It therefore will be useful for investigators to have a better understanding of how these two parameters differ in various organism types. In this study, the number of ribosomal operons and genome size were separately mapped onto a Bacterial phylogenetic tree.
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.