Reading Frame Retrieval of Genes: A New Parameter of Codon Usage Based on the Circular Code Theory

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Gene reading frame retrieval (RFR) is crucial for accurate protein synthesis.
• Codon usage patterns within a genome can influence RFR.
• Understanding RFR mechanisms across different life forms is essential.

Purpose of the Study:

• To introduce a novel function, f, for quantifying RFR based on codon usage.
• To investigate the relationship between RFR, gene size, and codon usage dispersion across diverse genomes.
• To explore the potential of RFR as a genomic classification tool.

Main Methods:

• Definition and application of the RFR function (f) across bacterial, eukaryotic, and archaeal genomes.
• Analysis of RFR as a function of mean codons per gene ([Formula: see text]).
• Spearman's rank correlation analysis between codon usage dispersion (d) and the RFR function (f).

Main Results:

• A universal property identified: RFR is enhanced in larger genes across all kingdoms.
• A strong negative correlation observed between codon usage dispersion and RFR (p-values < [Formula: see text] in bacteria, < [Formula: see text] in eukaryotes, < [Formula: see text] in archaea).
• The RFR function reveals a distinct genomic organization with a 'genome centre' and 'genome arms'.

Conclusions:

• Reading frame retrieval is enhanced by codon usage dispersion.
• The RFR function offers a new perspective on genome structure and organization.
• The RFR function holds potential for future genomic classification, alone or combined with other methods.