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Codon usage and bias among individual genes of the coccidia and piroplasms

Published online by Cambridge University Press:  06 April 2009

J. T. Ellis ,
D. A. Morrison ,
D. Avery  and
A. M. Johnson
J. T. Ellis
Affiliation:
Department of Microbiology, University of Technology Sydney, St Leonards Campus, P.O. Box 123 Broadway, New South Wales 2007, Australia
D. A. Morrison
Affiliation:
Department of Applied Biology, University of Technology Sydney, St Leonards Campus, P.O. Box 123 Broadway, New South Wales 2007, Australia
A. M. Johnson
Affiliation:
Department of Microbiology, University of Technology Sydney, St Leonards Campus, P.O. Box 123 Broadway, New South Wales 2007, Australia
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Summary

Codon usage has been analysed in individual gene sequences, derived from a variety of parasitic protozoa in the class Sporozoa of the phylum Apicomplexa using metric multidimensional scaling. The two groups of codon usage patterns detected reflect the two main subgroups of organisms studied (the coccidia and the piroplasms), and it is the pattern usage of synonymous codons that has the largest influence on overall codon usage in the individual genes, rather than being the pattern of amino acid composition of the gene product. The magnitude of the codon usage bias in the sequences was determined using three commonly used indices – NC', GC3s and B. In general, although relatively low levels of codon usage bias were detected in these gene sequences, codon usage bias does explain at least some of the codon usage patterns observed. Codon usage bias was observed to be dependent on the overall base composition of the genes analysed, which in turn was reflected in the types of codons that were either over-or under-represented in the nucleotide sequences. keeping with observations on prokaryotic organisms, it is speculated that the codon usage patterns detected in these parasitic protozoa are the result of directional mutation pressure on the base composition of the genomic DNA.

Keywords

BabesiaEimeriaTheileriaToxoplasmapiroplasmscoccidiacodon usage
Type
Research Article
Information
Parasitology , Volume 109 , Issue 3 , September 1994 , pp. 265 - 272
Copyright
Copyright © Cambridge University Press 1994

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