Mitreva, Makedonka and Wendl, Michael C and Martin, John and Wylie, Todd and Yin, Yong and Larson, Allan and Parkinson, John and Waterston, Robert H. and McCarter, James P. (2006) Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species. Genome Biology, 7.
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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.
| Item Type: | Article |
|---|---|
| Subjects: | Medical and Health Sciences > Basic medicine |
| Divisions: | Faculty of Medical Science |
| Depositing User: | Mirjana Kocaleva Vitanova |
| Date Deposited: | 30 Nov 2012 10:34 |
| Last Modified: | 13 Feb 2013 13:16 |
| URI: | https://eprints.ugd.edu.mk/id/eprint/2570 |
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