First analysis of synonymous codon usage in porcine circovirus

Area of Science:

• Virology
• Genomics
• Molecular Evolution

Background:

• Porcine circovirus (PCV) exists as PCV1 and PCV2.
• PCV2 is a significant pathogen impacting swine health and production.
• Understanding PCV codon usage is crucial for insights into its evolution.

Purpose of the Study:

• To investigate the codon usage bias in Porcine circovirus (PCV).
• To elucidate the evolutionary forces shaping codon usage in PCV1 and PCV2.

Main Methods:

• Genomic sequence analysis of PCV1 and PCV2.
• Effective Number of Codons (ENC) plot analysis.
• Neutrality plot analysis.
• Principal Component Analysis (PCA).

Main Results:

• Porcine circovirus (PCV) demonstrates very low codon usage bias.
• Mutational pressure significantly influences codon usage bias in PCV.
• Mutation bias dominates PCV1's codon usage, while PCV2 shows equal contribution from mutation bias and natural selection.
• Different open reading frames (ORFs) and dinucleotide patterns also affect PCV codon usage.

Conclusions:

• Codon usage bias in PCV is minimal.
• Mutational pressure is a key driver of codon usage patterns in PCV.
• Evolutionary forces differ slightly between PCV1 and PCV2.
• Findings contribute to understanding PCV evolution and genomic patterns.