Codon usage patterns in Nematoda: analysis based on over 25  million codons in thirty-two species.
BACKGROUND
Codon usage has direct utility in molecular characterization of species and is also a arker 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 ere 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 thenrapidly 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.


CONCLUSIONS
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.
Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63108, USA. mmitreva@watson.wustl.edu
Makedonka
M
Mitreva
Michael C
MC
Wendl
John
J
Martin
Todd
T
Wylie
Yong
Y
Yin
Allan
A
Larson
John
J
Parkinson
Robert H
RH
Waterston
James P
JP
McCarter
D000818:Animals; D001482:Base Composition; D002107:Caenorhabditis / Q000235:genetics; D017173:Caenorhabditis elegans / Q000235:genetics; D003062:Codon; D020224:Expressed Sequence Tags; D015801:Helminth Proteins / Q000737:chemistry / Q000235:genetics*; D009348:Nematoda / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny
D003062:Codon; D015801:Helminth Proteins