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Updated: Jun 28, 2026

High-Resolution Comparison of Bacterial Conjugation Frequencies

High-Resolution Comparison of Bacterial Conjugation Frequencies

Published on: January 10, 2019

Comparison of correspondence analysis methods for synonymous codon usage in bacteria.

Haruo Suzuki¹, Celeste J Brown, Larry J Forney

¹Department of Biological Sciences and Initiative for Bioinformatics and Evolutionary Studies, University of Idaho, PO Box 443051, Moscow, Idaho 83844-3051, USA. hsuzuki@uidaho.edu

DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes

|October 23, 2008

Summary

Within-group correspondence analysis (WCA) effectively reveals variations in synonymous codon usage across bacterial genomes. This method surpasses others, including relative synonymous codon usage (RSCU), in identifying usage patterns.

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Area of Science:

Genomics
Bioinformatics
Molecular Evolution

Background:

Synonymous codon usage (SCU) varies across organisms and genes due to factors like G+C content, replication strand skew, and gene expression.
Correspondence analysis (CA) is a common bioinformatics tool used to analyze SCU patterns and identify genes with unusual usage, such as horizontally transferred or highly expressed genes.

Purpose of the Study:

To comprehensively evaluate the effectiveness of four different CA methods for analyzing SCU variation in bacterial genomes.
To compare the performance of within-group CA (WCA) against other established CA methods, including those based on absolute codon frequency, relative codon frequency, and relative synonymous codon usage (RSCU).

Main Methods:

Applied four CA methods (absolute codon frequency, relative codon frequency, RSCU-based CA, and WCA) to analyze SCU in 241 bacterial genome sequences.
Evaluated the ability of each method to generate axes that accurately reflect variations in synonymous codon usage.

Main Results:

Within-group CA (WCA) demonstrated superior effectiveness in identifying major axes of variation in synonymous codon usage compared to the other three methods.
WCA identified previously unrecognized sources of SCU variation in certain genomes, such as replication strand skew in Rickettsia prowazekii.
CA based on relative synonymous codon usage (RSCU), while widely used, was found to be less effective than WCA.

Conclusions:

WCA is the most effective CA method for analyzing synonymous codon usage variation in bacterial genomes.
WCA offers enhanced power to detect subtle SCU patterns and their underlying causes, including those related to genomic features like replication strand skew.