MBE Advance Access published online on August 25, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl097
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1 Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK EH9 3JT
* To whom correspondence should be addressed. Despite the degeneracy of the genetic code, whereby different codons encode the same amino acid, alternative codons and amino acids are utilized non-randomly within and between genomes. Such biases in codon and amino acid usage have been demonstrated extensively in prokaryote genomes and likely reflect a balance between the action of mutation, selection, and genetic drift. Here, we quantify the effects of selection and mutation-drift as causes of codon and amino acid usage bias in a large collection of nematode partial genomes from 37 species spanning approximately 700 My of evolution, as inferred from expressed sequence tag (EST) measures of gene expression and from base composition variation. Average G+C content at silent sites among these taxa ranges from 10% to 63% and EST counts range more than 100-fold, underlying marked differences between the identities of major codons and optimal codons for a given species as well as influencing patterns of amino acid abundance among taxa. Few species in our sample demonstrate a dominant role of selection in shaping intra-genomic codon usage biases, and these are principally free-living rather than parasitic nematodes. This suggests that deviations in effective population size among species, with small effective sizes among parasites, are partly responsible for species differences in the extent to which selection shapes patterns of codon usage. Nevertheless, a consensus set of optimal codons emerges that is common to most taxa, indicating that, with some notable exceptions, selection for translational efficiency and accuracy favors similar sets of codons regardless of the major codon usage trends defined by base compositional properties of individual nematode genomes. No Genbank accession numbers are included. Five supplementary figures will accompany the manuscript; they are included at the end of this document.
Accepted August 23, 2006
Research Article
The Evolution of Biased Codon and Amino Acid Usage in Nematode Genomes
Asher D. Cutter 1 *, James D. Wasmuth 2, and Mark L. Blaxter 1
2 Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK EH9 3JT; present address : Department of Genetics and Genomic Biology, Hospital for Sick Children, 101 College St., Toronto, ON, M5G 1L7, Canada
Asher D. Cutter, E-mail: asher.cutter{at}utoronto.ca
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