近几十年来,通过深度测序技术和大数据分析的发展,在植物中发现了许多新出现或重新出现的RNA病毒。这些发现在很大程度上改变了我们对起源的理解,植物RNA病毒的进化和宿主范围。有证据表明它们的基因组成来源于病毒,宿主种群在植物RNA病毒的进化和宿主适应性中起着关键作用。在这个小型审查中,我们从组成偏差的角度描述了我们对植物RNA病毒进化的理解状态,并探索了它们如何适应宿主。似乎富含腺嘌呤(富含A)的编码序列,在绝大多数植物RNA病毒中发现低CpG和UpA二核苷酸频率和低密码子使用模式。植物RNA病毒的密码子使用模式受自然选择和突变压力的影响,主要来自寄主的自然选择是主导因素。密码子适应分析支持,植物RNA病毒可能在密码子适应和去优化之间进化出动态平衡,以在具有各种密码子使用模式的多个宿主中维持有效的复制循环。在未来,应解决植物RNA病毒的核苷酸组成和密码子使用的计算和实验分析的其他组合。
During recent decades, many new emerging or re-emerging RNA viruses have been found in plants through the development of deep-sequencing technology and big data analysis. These findings largely changed our understanding of the origin, evolution and host range of plant RNA viruses. There is evidence that their genetic composition originates from viruses, and host populations play a key role in the evolution and host adaptability of plant RNA viruses. In this mini-review, we describe the state of our understanding of the evolution of plant RNA viruses in view of compositional biases and explore how they adapt to the host. It appears that adenine rich (A-rich) coding sequences, low CpG and UpA dinucleotide frequencies and lower codon usage patterns were found in the vast majority of plant RNA viruses. The codon usage pattern of plant RNA viruses was influenced by both natural selection and mutation pressure, and natural selection mostly from hosts was the dominant factor. The codon adaptation analyses support that plant RNA viruses probably evolved a dynamic balance between codon adaptation and deoptimization to maintain efficient replication cycles in multiple hosts with various codon usage patterns. In the future, additional combinations of computational and experimental analyses of the nucleotide composition and codon usage of plant RNA viruses should be addressed.