Codon usage trajectories and 7-cluster structure of 143 complete bacterial genomic sequences

Abstract

Three results are presented. First, we prove the existence of a universal 7-cluster structure in all 143 completely sequenced bacterial genomes available in Genbank in August 2004, and explained its properties. The 7-cluster structure is responsible for the main part of sequence heterogeneity in bacterial genomes. In this sense, our 7 clusters is the basic model of bacterial genome sequence. We demonstrated that there are four basic ''pure'' types of this model, observed in nature: ''parallel triangles'', ''perpendicular triangles'', degenerated case and the flower-like type.Second, we answered the question: how big are the position-specific information and the contribution connected with correlations between nucleotide. The accuracy of the mean-field (context-free) approximation is estimated for bacterial genomes.We show that codon usage of bacterial genomes is a multi-linear function of their genomic G+C-content with high accuracy (more precisely, by two similar functions, one for eubacterial genomes and the other one for archaea). Description of these two codon-usage trajectories is the third result.All 143 cluster animated 3D-scatters are collected in a database and is made available on our web-site: http://www.ihes.fr/$zinovyev/7clusters.

Concurrent origins of the genetic code and the homochirality of life, and the origin and evolution of biodiversity. Part II: Technical appendix

“…And the 3 rd position GC content declined rapidly from the highest to the lowest in the evolution direction when the total GC content declines. The GC content variation in the simulation agrees with the observation (to compare Fig S2b2 with Figure 2 in [14] and Figure 5 in [15]), so the recruitment order obtained by the roadmap is reasonable. The recruitment order of the codons by the roadmap generally agree with the order in [4] [16] [17].…”

Genetic code evolution as an initial driving force for molecular evolution

“…6e, we can observe a step in the middle of the line corresponding to the first codon position and a junction between lines corresponding to the first and second codon positions; these characters of step and junction can also be observed in the plots based on biological data [16][8] [17]. The slope of the line corresponding to the third codon position is the deepest, because G and C occupy all the third positions of the earliest codons for 20 amino acids, and A and U occupy all the third position of the latest codons for 20 amino acids, but their compositions are about invariant for the first and second positions (Tab.…”

The Mystery of Two Straight Lines in Bacterial Genome Statistics

“…Some hints to observed structure were reported recently in studies on multivariate analysis of bacterial codon usage (for example, see Figure 6 from [8], or in codon bias study in [14]). Some other illustrations can be found in our publications [15][16][17] and on the web-site [18]. : PCA plots for the average codon usage and the corresponding meanfield approximations for 348 bacterial genomes; top-left: PCA plot of the average codon usage; top-right: projection on the linear envelope of principal components calculated for the average codon usage and the corresponding mean-field approximations taken together; bottom-left: projection on the linear envelope of principal components calculated for the mean-field approximations only.…”