Codon usage bias is presumably affected by tRNA selection effects in Actinidia polyploidization events

Area of Science:

• Genomics
• Molecular Evolution
• Bioinformatics

Background:

• Polyploidization is a key speciation mechanism, but its impact on synonymous codon frequencies and codon usage bias (CUB) is not fully understood.
• Investigating CUB patterns in Actinidia polyploidization events is crucial for understanding genome evolution.

Purpose of the Study:

• To determine if polyploidization events alter codon usage bias (CUB) in Actinidia species.
• To identify the primary factors influencing CUB variation in Actinidia and related plant species.

Main Methods:

• Comparative genomic analysis of CUB across seven Actinidia species (two polyploid, five diploid) and five related species (one polyploid, four diploid).
• Analysis of GC content, effective number of codons (ENC), GC3s, relative synonymous codon usage (RSCU), and tRNA adaptation index (tAI).

Main Results:

• All analyzed genomes showed a preference for A/T-rich nucleotides and codons.
• Natural selection, rather than polyploidization, was identified as the main driver of CUB variation, indicated by ENC and GC3s distribution.
• Actinidia species exhibited stronger correlations between ENC and tAI, suggesting a more significant role of tRNA availability in shaping CUB compared to non-Actinidia species.

Conclusions:

• Codon usage bias in Actinidia is shaped by natural selection and influenced by tRNA availability, not polyploidization events.
• The findings provide insights into the evolutionary forces governing gene expression and genome evolution in polyploid plants.