Deciphering codon usage patterns in six Quercus genome

Codon usage bias (CUB) affects translation efficiency and accuracy, but genome-wide CUB patterns in Quercus (a genus of ~ 450 ecologically vital species) remain uncharacterized, with prior studies limited to chloroplast genomes. Here, we conducted the first whole-genome CUB analysis of six Quercus species (Q. acutissima, Q. suber, Q. dentata, Q. robur, Q. lobata, Q. mongolica) using bioinformatics tools. We calculated effective number of codons (ENC), relative synonymous codon usage (RSCU), and GC content, and applied neutrality plots, parity plots (PR2), ENC-GC3s plots, and translational selection (P2) analyses. Results showed genomic GC content ranged 42.25% (Q. robur)–46.2% (Q. suber), with ENC values (51.777–52.843) indicating weak CUB. Multi-method analyses confirmed natural selection is the dominant driver of CUB (mutation pressure had minor effects). All six species preferentially used AGA (Arginine), UCU (Serine), and CCA (Glycine). This study fills a gap in Quercus genomic research, clarifies CUB evolutionary drivers, and identifies conserved preferred codons—providing a basis for Quercus molecular breeding and transgenic optimization.