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

Mahin Pouresmaeil1, Shahnam Azizi-Dargahlou2

  • 1Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran.

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|March 4, 2024
PubMed
Summary

Cauliflower mosaic virus (CaMV) exhibits codon usage bias, adapting its genes to host organisms like Brassica oleracea and Brassica rapa. Natural selection is the main driver of this adaptation, ensuring efficient viral replication and spread.

Keywords:
CaMVcodon adaptationco‐evolutionphylogeographyvirus–host interaction

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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.