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DNA Research Advance Access originally published online on October 21, 2008
DNA Research 2008 15(6):357-365; doi:10.1093/dnares/dsn028
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© The Author 2008. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria

Haruo Suzuki*, Celeste J. Brown, Larry J. Forney and Eva M. Top

Department of Biological Sciences and Initiative for Bioinformatics and Evolutionary Studies, University of Idaho, PO Box 443051, Moscow, Idaho 83844-3051

Received 21 June 2008 ; accepted 24 September 2008.

Synonymous codon usage varies both between organisms and among genes within a genome, and arises due to differences in G + C content, replication strand skew, or gene expression levels. Correspondence analysis (CA) is widely used to identify major sources of variation in synonymous codon usage among genes and provides a way to identify horizontally transferred or highly expressed genes. Four methods of CA have been developed based on three kinds of input data: absolute codon frequency, relative codon frequency, and relative synonymous codon usage (RSCU) as well as within-group CA (WCA). Although different CA methods have been used in the past, no comprehensive comparative study has been performed to evaluate their effectiveness. Here, the four CA methods were evaluated by applying them to 241 bacterial genome sequences. The results indicate that WCA is more effective than the other three methods in generating axes that reflect variations in synonymous codon usage. Furthermore, WCA reveals sources that were previously unnoticed in some genomes; e.g. synonymous codon usage related to replication strand skew was detected in Rickettsia prowazekii. Though CA based on RSCU is widely used, our evaluation indicates that this method does not perform as well as WCA.

Key words: correspondence analysis; synonymous codon usage; horizontal gene transfer; strand-specific mutational bias; translational selection

* To whom correspondence should be addressed. Tel. +1 208-885-8858. Fax. +1 208-885-7905. E-mail: hsuzuki{at}uidaho.edu

Edited by Hiroyuki Toh


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