ArticleGenome biology2006
An environmental signature for 323 microbial genomes based on codon adaptation indices.
Article in Genome biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 62 citations in OpenAlex.
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- Compression rates of microbial genomes are associated with genome size and base composition.Genomics & informatics · 2024Article
- Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis.NPJ biofilms and microbiomes · 2023Article
- Hydrological properties predict the composition of microbial communities cycling methane and nitrogen in rivers.ISME communications · 2022Article
- Genome mining reveals abiotic stress resistance genes in plant genomes acquired from microbesFrontiers in plant science · 2022Article
- Comparison of compositional constraints: Nuclear genome vs plasmid genome of Pseudomonas syringae pv. tomato DC3000.Journal of biosciences · 2022Article
- Whole Genome Sequencing and Comparative Genomic Analyses ofMicroorganisms · 2020Article
- Evolution of Genomic Base Composition: From Single Cell Microbes to Multicellular Animals.Computational and structural biotechnology journal · 2019Review
- Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes.Frontiers in microbiology · 2019Article
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- Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes.Nature communications · 2018Article
- Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer.International journal of molecular sciences · 2016Article
- Coevolution mechanisms that adapt viruses to genetic code variations implemented in their hosts.Journal of genetics · 2016Article
- Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors.BioMed research international · 2015Article
- Analysis of synonymous codon usage patterns in the genus Rhizobium.World journal of microbiology & biotechnology · 2013Article
- Translation Elongation Rate Measurement of Epstein-Barr Virus Strain GD1.Iranian journal of cancer prevention · 2013Article
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- Microbial lifestyle and genome signatures.Current genomics · 2012Article
- Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage.PloS one · 2012Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCodon 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.
resultsThe 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.
conclusionThe 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.
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