Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species

Makedonka Mitreva¹ , Michael C Wendl¹ , John Martin¹ , Todd Wylie¹ , Yong Yin¹ , Allan Larson² , John Parkinson³ , Robert H Waterston⁴ and James P McCarter¹^,5

¹Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63108, USA

²Department of Biology, Washington University, St. Louis, Missouri 63130, USA

³Hospital for Sick Children, Toronto, and Departments of Biochemistry/Medical Genetics and Microbiology, University of Toronto, M5G 1X8, Canada

⁴Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA

⁵Divergence Inc., St Louis, Missouri 63141, USA

author email corresponding author email

Genome Biology 2006, 7:R75doi:10.1186/gb-2006-7-8-r75


Published:	14 August 2006

Subject areas: Molecular biology, Evolution, Genetics

Abstract

Background

Codon usage has direct utility in molecular characterization of species and is also a marker for molecular evolution. To understand codon usage within the diverse phylum Nematoda, we analyzed a total of 265,494 expressed sequence tags (ESTs) from 30 nematode species. The full genomes of Caenorhabditis elegans and C. briggsae were also examined. A total of 25,871,325 codons were analyzed and a comprehensive codon usage table for all species was generated. This is the first codon usage table available for 24 of these organisms.

Results

Codon usage similarity in Nematoda usually persists over the breadth of a genus but then rapidly diminishes even within each clade. Globodera, Meloidogyne, Pristionchus, and Strongyloides have the most highly derived patterns of codon usage. The major factor affecting differences in codon usage between species is the coding sequence GC content, which varies in nematodes from 32% to 51%. Coding GC content (measured as GC3) also explains much of the observed variation in the effective number of codons (R = 0.70), which is a measure of codon bias, and it even accounts for differences in amino acid frequency. Codon usage is also affected by neighboring nucleotides (N1 context). Coding GC content correlates strongly with estimated noncoding genomic GC content (R = 0.92). On examining abundant clusters in five species, candidate optimal codons were identified that may be preferred in highly expressed transcripts.

Conclusion

Evolutionary models indicate that total genomic GC content, probably the product of directional mutation pressure, drives codon usage rather than the converse, a conclusion that is supported by examination of nematode genomes.