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<p>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 <i>Quercus</i> species (<i>Q. acutissima</i>,<i> Q. suber</i>,<i> Q. dentata</i>,<i> Q. robur</i>,<i> Q. lobata</i>,<i> Q. mongolica</i>) 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% (<i>Q. robur</i>)–46.2% (<i>Q. suber</i>), 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 <i>Quercus</i> genomic research, clarifies CUB evolutionary drivers, and identifies conserved preferred codons—providing a basis for <i>Quercus</i> molecular breeding and transgenic optimization.</p>

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Deciphering codon usage patterns in six Quercus genome

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月17日

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  • Yuyang Zhang,
  • Yunqi Ma,
  • Jian Gao,
  • Tao Yu

摘要

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.