Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable disease resistance. In addition to the evolutionary forces of mutation, recombination and reassortment, factors such as climate, agriculture practices and the presence of DNA satellites may impact viral diversity. To gain insight into the factors that alter and shape viral diversity in planta, we used high-throughput sequencing to characterize the accumulation of nucleotide diversity after inoculation of infectious clones corresponding to African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in the susceptible cassava landrace Kibandameno. We found that vegetative propagation had a significant effect on viral nucleotide diversity, while temperature and a satellite DNA did not have measurable impacts in our study. EACMCV diversity increased linearly with the number of vegetative propagation passages, while ACMV diversity increased for a time and then decreased in later passages. We observed a substitution bias toward C→T and G→A for mutations in the viral genomes consistent with field isolates. Non-coding regions excluding the promoter regions of genes showed the highest levels of nucleotide diversity for each genome component. Changes in the 5′ intergenic region of DNA-A resembled the sequence of the cognate DNA-B sequence. The majority of nucleotide changes in coding regions were non-synonymous, most with predicted deleterious effects on protein structure, indicative of relaxed selection pressure over six vegetative passages. Overall, these results underscore the importance of knowing how cropping practices affect viral evolution and disease progression.

中文翻译：

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木薯花叶病毒的种群多样性在连续营养繁殖过程中增加

木薯花叶病 (CMD) 对木薯构成严重威胁，木薯是 3 亿多非洲人的主要块根作物。CMD 是由快速进化的单链 DNA 病毒引起的，因此很难形成持久的抗病能力。除了突变、重组和重配的进化力量之外，气候、农业实践和 DNA 卫星的存在等因素也可能影响病毒多样性。为了深入了解改变和塑造植物病毒多样性的因素，我们使用高通量测序来表征接种与非洲木薯花叶病毒（ACMV）和东非木薯花叶喀麦隆病毒相对应的感染性克隆后核苷酸多样性的积累。 EACMCV）存在于易受影响的木薯地方品种 Kibandameno 中。我们发现营养繁殖对病毒核苷酸多样性有显着影响，而温度和卫星 DNA 在我们的研究中没有可测量的影响。EACMCV多样性随营养繁殖传代次数线性增加，而ACMV多样性在一段时间内增加，然后在以后的传代中减少。我们观察到病毒基因组突变存在 C→T 和 G→A 的替代偏差，与现场分离株一致。除基因启动子区域外的非编码区域显示每个基因组组件的核苷酸多样性水平最高。DNA-A 5' 基因间区域的变化与同源 DNA-B 序列的序列相似。编码区的大多数核苷酸变化都是非同义的，大多数对蛋白质结构具有预测的有害影响，表明在六次营养传代中选择压力有所放松。总的来说，这些结果强调了了解种植方式如何影响病毒进化和疾病进展的重要性。