Genomic factors shaping codon usage across the Saccharomycotina subphylum.

Area of Science:

• Genomics
• Molecular Evolution
• Bioinformatics

Background:

• Codon usage bias, the non-uniform use of synonymous codons, impacts gene expression and is shaped by various forces.
• Understanding codon usage patterns in fungi, particularly the Saccharomycotina subphylum, is crucial for deciphering evolutionary mechanisms and cellular functions.

Purpose of the Study:

• To characterize codon usage bias across 1,154 strains from 1,051 Saccharomycotina species.
• To investigate the molecular mechanisms, evolutionary drivers, and genomic features contributing to these biases.
• To explore the impact of translational selection and identify lineage-specific codon usage patterns.

Main Methods:

• Comparative genomic analysis of codon usage patterns across diverse fungal species.
• Machine learning algorithms for classifying yeast orders based on codon usage bias.
• Analysis of gene expression, tRNA repertoire, and genomic features (GC content, genome length, BUSCO count).

Main Results:

• A general preference for A/T-ending codons was observed, correlated with GC content and tRNA-ome size.
• Codon usage bias allowed for >90% accurate classification of yeast orders.
• Extreme codon usage bias in Saccharomycodales linked to a deficiency in arginine tRNAs decoding CGN codons.

Conclusions:

• Codon usage bias in Saccharomycotina is shaped by genomic features and GC content, as well as translational selection.
• The Saccharomycodales exhibit unique codon usage patterns driven by a decline in arginine tRNA function.
• Additional evolutionary forces beyond known factors contribute to specific codon preferences and avoidance in yeast lineages.