Analysis of codon usage patterns of bacterial genomes using the self-organizing map

Area of Science:

• Genomics
• Bioinformatics
• Microbial Evolution

Background:

• Codon usage patterns exhibit significant variation across species and within individual genomes.
• Previous research utilized codon usage to identify highly expressed and horizontally transferred genes in Escherichia coli.
• Understanding these patterns is crucial for deciphering gene function and evolutionary history.

Purpose of the Study:

• To analyze codon usage patterns in seven microbial genomes (Escherichia coli, Aquifex aeolicus, Archaeoglobus fulgidus, Haemophilus influenzae RD:, Methanococcus jannaschii, Methanobacterium thermoautotrophicum, and Pyrococcus horikoshii).
• To identify highly expressed genes and horizontally transferred genes using Kohonen's self-organizing map.
• To investigate the origins of horizontally transferred genes and environmental adaptations in thermophilic organisms.

Main Methods:

• Application of Kohonen's self-organizing map algorithm.
• Analysis of codon usage patterns across seven diverse microbial genomes.
• Clustering of average codon usage for main gene categories and functional classification of genes.

Main Results:

• All analyzed genomes showed a distinct category of horizontally transferred genes, ranging from 7.7% to 21.4%.
• The proportion of highly expressed genes varied from 0% to 11.8% across the genomes.
• A notable mixing of gene classes in thermophilic organisms suggests shared origins for horizontally transferred genes and environmental adaptation.

Conclusions:

• Horizontally transferred genes are prevalent across the studied microbial genomes.
• Genes involved in communication and structure are more frequently horizontally transferred than those related to information processing or energy metabolism.
• Codon usage analysis provides valuable insights into gene transfer events and adaptive strategies in microbial evolution.