Investigation of CaMV-host co-evolution through synonymous codon pattern.

Area of Science:

• Virology
• Molecular Biology
• Genomics

Background:

• Cauliflower mosaic virus (CaMV) is a globally distributed plant virus with a double-stranded DNA genome.
• Phylogenetic analysis reveals two main groups of CaMV isolates, with Iranian strains exhibiting significant genetic diversity.

Purpose of the Study:

• To investigate the codon usage bias in CaMV and its relationship with host organisms.
• To identify the evolutionary forces driving codon usage patterns in CaMV.

Main Methods:

• Phylogenetic analysis of 121 CaMV isolates.
• Dinucleotide odds ratio analysis and Relative Synonymous Codon Usage (RSCU) analysis.
• Codon Adaptation Index (CAI) and Relative Codon Deoptimization Index (RCDI) calculations.
• Effective Number of Codons (ENC)-plot and neutrality plot analysis.

Main Results:

• Nucleotide A is the most abundant (36.95%) in the CaMV genome; TC dinucleotides are overrepresented, while CG dinucleotides are underrepresented.
• CaMV shows significant codon usage bias, with evidence of adaptation to susceptible hosts like Brassica oleracea and Brassica rapa (CAI > 0.8).
• Genes encoding reverse transcriptase and coat proteins have the highest CAI (0.83), indicating optimized expression for virion production.
• Natural selection is identified as the primary factor influencing CaMV codon usage bias.

Conclusions:

• CaMV genes have co-evolved with their hosts, optimizing gene expression for efficient infection and spread.
• The study highlights the role of natural selection in shaping viral codon usage and adaptation.
• Understanding CaMV's molecular mechanisms can inform strategies for disease management in cruciferous crops.