Exploring Codon Usage Patterns and Influencing Factors in Ranavirus DNA Polymerase Genes

Area of Science:

• Virology
• Bioinformatics
• Evolutionary Biology

Background:

• Ranaviruses pose a significant global threat to amphibians and other cold-blooded vertebrates.
• Understanding viral gene evolution is crucial for managing Ranavirus emergence.

Purpose of the Study:

• To investigate codon usage patterns in Ranavirus DNA polymerase genes using bioinformatics.
• To identify factors influencing codon usage bias and host adaptation in Ranaviruses.

Main Methods:

• Analysis of 61 DNA polymerase genes from various ranaviruses.
• Assessment of relative synonymous codon usage (RSCU) and codon adaptation index (CAI).
• Correlation analysis including nucleotide content, effective number of codons (ENC), and neutrality plots.

Main Results:

• Ranavirus DNA polymerase genes show a low codon usage bias.
• Codon usage is primarily driven by natural selection, with a preference for codons ending in C or G.
• Analysis indicates robust host adaptability and significant host selection pressure on viral genes.

Conclusions:

• Natural selection is the dominant force shaping codon usage in Ranavirus DNA polymerase genes.
• Ranaviruses demonstrate significant adaptation to their hosts, driven by evolutionary pressures.
• Findings provide insights into the evolution and adaptation mechanisms of Ranaviruses.