Visualization of ribosomal RNA operon copy number distribution

BackgroundResults 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.ResultsA 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.ConclusionOnce 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.

[1]  T. Schmidt,et al.  Life History Implications of rRNA Gene Copy Number in Escherichia coli , 2004, Applied and Environmental Microbiology.

[2]  F. Rodríguez-Valera,et al.  Intragenomic 16S rDNA Divergence in Haloarcula marismortui Is an Adaptation to Different Temperatures , 2007, Journal of Molecular Evolution.

[3]  James R. Cole,et al.  rrndb: the Ribosomal RNA Operon Copy Number Database , 2001, Nucleic Acids Res..

[4]  G. Fox,et al.  Phylogenetic mapping of bacterial morphology. , 1998, Microbiology.

[5]  Les Dethlefsen,et al.  Performance of the Translational Apparatus Varies with the Ecological Strategies of Bacteria , 2007, Journal of bacteriology.

[6]  Thomas M. Schmidt,et al.  rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea , 2008, Nucleic Acids Res..

[7]  Kangseok Lee,et al.  Heterogeneous rRNAs are differentially expressed during the morphological development of Streptomyces coelicolor. , 2007, FEMS microbiology letters.

[8]  Sean R. Eddy,et al.  ATV: display and manipulation of annotated phylogenetic , 2001, Bioinform..

[9]  J. Eisen,et al.  A simple, fast, and accurate method of phylogenomic inference , 2008, Genome Biology.

[10]  I. Thorseth,et al.  Enumeration of Archaea and Bacteria in seafloor basalt using real-time quantitative PCR and fluorescence microscopy. , 2008, FEMS microbiology letters.

[11]  T. Schmidt,et al.  rRNA Operon Copy Number Reflects Ecological Strategies of Bacteria , 2000, Applied and Environmental Microbiology.

[12]  E. Stackebrandt,et al.  Clostridium paradoxum DSM 7308T contains multiple 16S rRNA genes with heterogeneous intervening sequences. , 1996, Microbiology.

[13]  Turova Tp,et al.  Copy number of ribosomal operons in prokaryotes and its effect on phylogenic analyses , 2003 .

[14]  S. Acinas,et al.  Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple rrn Operons , 2004, Journal of bacteriology.

[15]  T. Tourova,et al.  Copy Number of Ribosomal Operons in Prokaryotes and Its Effect on Phylogenetic Analyses , 2004, Microbiology.

[16]  P. Dennis,et al.  Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui. , 1992, Genetics.