Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization

PLoS Comput Biol. 2006 Jan;2(1):e2. doi: 10.1371/journal.pcbi.0020002. Epub 2006 Jan 13.


Genome organization can be studied through analysis of chromosome position-dependent patterns in sequence-derived parameters. A comprehensive analysis of such patterns in prokaryotic sequences and genome-scale functional data has yet to be performed. We detected spatial patterns in sequence-derived parameters for 163 chromosomes occurring in 135 bacterial and 16 archaeal organisms using wavelet analysis. Pattern strength was found to correlate with organism-specific features such as genome size, overall GC content, and the occurrence of known motility and chromosomal binding proteins. Given additional functional data for Escherichia coli, we found significant correlations among chromosome position dependent patterns in numerous properties, some of which are consistent with previously experimentally identified chromosome macrodomains. These results demonstrate that the large-scale organization of most sequenced genomes is significantly nonrandom, and, moreover, that this organization is likely linked to genome size, nucleotide composition, and information transfer processes. Constraints on genome evolution and design are thus not solely dependent upon information content, but also upon an intricate multi-parameter, multi-length-scale organization of the chromosome.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / genetics
  • Base Sequence
  • Cell Shape
  • Chromosomes, Bacterial / genetics*
  • Databases, Genetic
  • Evolution, Molecular*
  • Gene Expression Regulation, Bacterial
  • Genome, Bacterial / genetics*
  • Nuclear Proteins / genetics
  • Species Specificity


  • Bacterial Proteins
  • Nuclear Proteins