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Selection on codon usage and amino acid sequences in prokaryotes

Friday, November 08, 2013 — Poster Session III

10:00 a.m. – 12:00 p.m.

FAES Academic Center (Upper-Level Terrace)




  • W. Ran
  • D.M. Kristensen
  • E.V. Koonin


We examined the relationship between the selection affecting codon usage and selection on protein sequences for orthologous genes from closely related prokaryotic genomes representing 1390 species from diverse lineages of archaea and bacteria that are included in the Alignable Tight Genome Clusters (ATGC) database. The codon usage bias is low: 63.7% of Fopt are below 0.55. This relatively weak selection on codon usage contrasts the strong purifying selection on amino acid sequences, with 64.6% of the dN/dS values being below 0.1. In all analyzed bacteria and archaea, genes that are subject to strong purifying selection on amino acid sequences show a wide spread of codon bias. Nevertheless, for most of the compared genomes, a weak but statistically significant negative correlation between Fopt and dN/dS in was observed indicative of a link between selection affecting protein sequence and selection on codon usage. An even weaker correlation is found in 45 pathogens that generally evolve under weak constraints when compared with 44 non-pathogens. The genes related to metabolism showed a stronger connection between the two aspects of selection than genes encoding proteins involved in information storage and processing. The biology behind these correlations is discussed.

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