Genome-Wide Analysis of Codon Usage Bias of Pseudorabies Virus (PRV)-Responsive Porcine Genes Based on Transcriptome Data

Pseudorabies virus (PRV) causes Aujeszky’s disease and continues to pose a potential threat to the swine industry. Understanding the codon usage patterns of PRV-responsive porcine genes could shed light on host–virus interactions, evolutionary pressure, and gene expression optimization. In this study, we characterized the codon usage bias (CUB) of 77 PRV-responsive porcine genes identified from published RNA-seq data of PRV type II-infected cells. CUB analysis showed that the compositional bias influenced codon bias. Overall percent T composition is the lowest among all nucleotides. The analyzed genes were GC-rich, with mean GC and GC3s contents of 56.75% and 68.31%, respectively, and generally favored G/C-ending synonymous codons. Odds ratio reveals the overrepresentation of CpT, TpG, and the depletion of TpA. PCA, codon-shuffling, and matched-control analyses further indicated that nucleotide composition, particularly at the third codon position, contributed strongly to the major variation in synonymous codon usage, with 34 of 59 codons differing significantly from length-matched genomic backgrounds. Compared with average Sus scrofa codon usage and length-matched control sets, the codon usage profile of the PRV-responsive porcine genes was significantly shifted, and the neutrality-plot slope of 0.245 (95% CI: 0.157–0.334) was typical of porcine genes. The ENC-GC3s analysis showed substantial deviation from the expected curve, and matched-control analyses confirmed that the GC3 enrichment and codon-usage shift persisted after controlling for gene length and expression status. Overall, these results reveal a GC3-enriched codon usage pattern among porcine host genes strongly induced during PRV infection, significantly shifted relative to matched genomic backgrounds, and provide a basis for further investigation of host–virus interactions, translational regulation, and sequence optimization in PRV-related research.