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Resources » Paper

James P McCarter et al. (2005) International Worm Meeting "Codon usage patterns in Nematoda: analysis based upon 26 million codons in 32 species"

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  • Comments on James P McCarter et al. (2005) International Worm Meeting "Codon usage patterns in Nematoda: analysis based upon 26 million codons in 32 species" (0)

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    Status:
    Publication type:
    Meeting_abstract
    WormBase ID:
    WBPaper00025606

    James P McCarter, M Mitreva, Mc Wendel, T Wylie, J Parkinson, M Blaxter, & R H Waterston (2005). Codon usage patterns in Nematoda: analysis based upon 26 million codons in 32 species presented in International Worm Meeting. Unpublished information; cite only with author permission.

    Codon usage has direct utility in molecular characterization of a species and also serves as a marker for molecular evolution. In order to better understand codon usage within the diverse phylum Nematoda, we analyzed a total of 265,494 ESTs in 93,645 clusters from 30 nematode species. Putative translations, obtainable for 75% of clusters, were based upon homology to known or predicted proteins. The full genomes of Caenorhabditis elegans and C. briggsae were also examined. A total of 25,871,325 codons were analyzed and a definitive codon usage table for all species was generated. Similarity in codon usage can be quantified by the chi-square statistic. Related nematodes have previously been observed to have similar codon usage but the evolutionary distances at which conservation diminishes had not been established. We show that codon usage similarity in Nematoda is a short-range phenomenon, generally persisting over the breadth of a genus but then rapidly diminishing within each clade. A second focus was the underlying factors that bias codon usage. In comparing species, we find a strong correlation between the overall AT/GC content of the genome and similarity in codon usage. Surprising, differences exist among species and clades in the degree of codon-usage bias as measured by effective number of codons (ENC), indicating potential differences in selective pressures or population dynamics. This study was supported by NIH-NIAID AI-46593.

    Affiliations:
    - Hospital For Sick Children, Toronto Canada
    - Univ. of Washington, WA, USA
    - Genome Sequencing Center, Washington Univ., St. Louis, MO, USA 63108
    - Divergence, Inc., St. Louis, MO, USA
    - Univ. of Edinburgh, UK


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