Organisms can essentially be classified according to two codon patterns.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Previous classification of 23 bacteria into S-type (Staphylococcus aureus) and E-type (Escherichia coli) based on amino acid concentrations.
• Amino acid composition and nucleotide content are key genomic features.

Purpose of the Study:

• To investigate prokaryotic and eukaryotic genome structures using amino acid compositions and nucleotide contents.
• To classify a broader range of organisms based on genomic features.

Main Methods:

• Cluster analysis of GC content at the third codon position for 112 bacteria, 15 archaea, and 18 eukaryotes.
• Calculation of amino acid concentrations and nucleotide contents from complete genomes.
• Correlation analysis between amino acid concentrations and nucleotide content.

Main Results:

• Classification of 145 organisms into AT-type (high A/T, low G/C) and GC-type (high G/C, low A/T) based on third codon position.
• Synchronous reciprocal changes in nucleotide content at the third codon position across organisms.
• Differential correlations between amino acid concentrations (Ala, Ile, Lys) and GC content across bacteria, archaea, and eukaryotes, suggesting distinct evolutionary trajectories.

Conclusions:

• All organisms are fundamentally classifiable into two groups based on characteristic codon patterns (AT-type and GC-type).
• Distinct evolutionary pathways for bacteria, archaea, and eukaryotes are reflected in their genomic composition and amino acid-nucleotide correlations.
• Genomic analysis of nucleotide content and amino acid composition provides insights into organismal classification and evolution.