An environmental signature for 323 microbial genomes based on codon adaptation indices

Hanni Willenbrock, Carsten Friis, Agnieszka Juncker, David Ussery

    Research output: Contribution to journalJournal articleResearchpeer-review

    203 Downloads (Pure)


    Background: Codon adaptation indices ( CAIs) represent an evolutionary strategy to modulate gene expression and have widely been used to predict potentially highly expressed genes within microbial genomes. Here, we evaluate and compare two very different methods for estimating CAI values, one corresponding to translational codon usage bias and the second obtained mathematically by searching for the most dominant codon bias. Results: The level of correlation between these two CAI methods is a simple and intuitive measure of the degree of translational bias in an organism, and from this we confirm that fast replicating bacteria are more likely to have a dominant translational codon usage bias than are slow replicating bacteria, and that this translational codon usage bias may be used for prediction of highly expressed genes. By analyzing more than 300 bacterial genomes, as well as five fungal genomes, we show that codon usage preference provides an environmental signature by which it is possible to group bacteria according to their lifestyle, for instance soil bacteria and soil symbionts, spore formers, enteric bacteria, aquatic bacteria, and intercellular and extracellular pathogens. Conclusion: The results and the approach described here may be used to acquire new knowledge regarding species lifestyle and to elucidate relationships between organisms that are far apart evolutionarily.
    Original languageEnglish
    JournalGenome Biology
    Issue number12
    Pages (from-to)R114
    Publication statusPublished - 2006


    Dive into the research topics of 'An environmental signature for 323 microbial genomes based on codon adaptation indices'. Together they form a unique fingerprint.

    Cite this