Wang Jiuli, Lu Xinhang, Dong Jiaying, Liu Jiaqian, Guo Borui, Zhang Chen, Liu Jing, Wang Hongxia
College of Ecological Environment and Resources, Qinghai Minzu University, Xining 810007, China.
State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining 810016, China.
Biology (Basel). 2025 May 9;14(5):524. doi: 10.3390/biology14050524.
Wheat dwarf virus (WDV) poses significant threats to gramineous crops, making it crucial to explore its codon usage patterns and evolutionary dynamics for effective disease control. This study analyzed ten WDV isolates, including two from triticale (WDVT_117 and WDVT_118), using metrics such as relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), and codon bias index (CBI). Neutrality plots, ENC-plots, and PR2-plots were employed to assess the role of mutation and selection. Results revealed weak codon preference in triticale-derived strains (CAI: 0.145-0.269; CBI: -0.042-0.111; ENC > 40), with hierarchical GC content. Neutrality analysis and ENC-plot distributions indicated natural selection as the dominant force, supported by T/C bias at the third codon position (PR2-plot). Shared optimal codons UUC and UAC in highly expressed genes may imply a potential significant role in virus adaptation. RSCU-based clustering and MP phylogenetic analysis revealed that WDVT strains form a distinct cluster with elevated genetic diversity, potentially driven by genomic recombination in the synthetic host. These findings demonstrate that WDVT balances mutational constraints and host adaptation through selective codon optimization. This study provides a foundation for codon-based antiviral research and the development of agricultural strategies to combat WDV infections.
小麦矮缩病毒（WDV）对禾本科作物构成重大威胁，因此探索其密码子使用模式和进化动态对于有效控制病害至关重要。本研究分析了10个WDV分离株，其中包括来自小黑麦的两个分离株（WDVT_117和WDVT_118），使用了相对同义密码子使用（RSCU）、有效密码子数（ENC）、密码子适应指数（CAI）和密码子偏好指数（CBI）等指标。利用中性绘图、ENC绘图和PR2绘图来评估突变和选择的作用。结果显示，小黑麦衍生菌株的密码子偏好较弱（CAI：0.145 - 0.269；CBI： - 0.042 - 0.111；ENC > 40），GC含量呈分层分布。中性分析和ENC绘图分布表明自然选择是主导力量，第三密码子位置的T/C偏好（PR2绘图）也支持这一点。高表达基因中共享的最优密码子UUC和UAC可能暗示其在病毒适应中具有潜在的重要作用。基于RSCU的聚类和MP系统发育分析表明，WDVT菌株形成了一个具有较高遗传多样性的独特聚类，这可能是由合成宿主中的基因组重组驱动的。这些发现表明，WDVT通过选择性密码子优化来平衡突变限制和宿主适应。本研究为基于密码子的抗病毒研究以及制定防治WDV感染的农业策略奠定了基础。
