The diversification of begomovirus populations is predominantly driven by mutational dynamics.
The diversification of begomovirus populations is predominantly driven by mutational dynamics.
复制标题
DOI：
10.1093/ve/vex005
复制
发表时间：
2017-01
期刊：
影响因子：
5.3
通讯作者：
Zerbini FM
中科院分区：
文献类型：
--
作者：
Lima ATM;Silva JCF;Silva FN;Castillo-Urquiza GP;Silva FF;Seah YM;Mizubuti ESG;Duffy S;Zerbini FM
Begomoviruses（单链DNA植物病毒）是造成严重农业威胁的原因。菜豆病毒种群表现出高度的宿主内遗传变异，并与RNA病毒一样迅速地进化。尽管菜豆花叶病毒属的重组倾向性已被广泛证实，但重组和突变对菜豆花叶病毒属种群遗传变异的相对贡献尚未得到评估。我们估计了来自世界各地的Begomovirus数据集的遗传变异性。从我们的分析中可以明显看出，由于重组，cp和rep基因长度上的遗传变异分布不均匀。为了估计重组和突变对菜豆花叶病毒遗传变异性的相对贡献，我们将所有替换映射到最大似然树上，并计算与重组（ηr）和突变（ημ）相关的分支上的替换数。此外，我们还估计了每代两种进化机制的相对速率（r/μ），以表达相对于突变，菜豆花叶病毒基因组受重组影响的频率。我们观察到，在所有的菜豆花叶病毒数据集的遗传变异的组成是由突变占主导地位。此外，估计值之间的低相关性表明重组和突变的相对贡献不一定是其相对速率的函数。我们的研究结果表明，虽然相当一部分的遗传变异水平可以分配到重组，它总是低于由于突变，表明菜豆花叶病毒种群的多样化主要是由突变动力学驱动。
Begomoviruses (single-stranded DNA plant viruses) are responsible for serious agricultural threats. Begomovirus populations exhibit a high degree of within-host genetic variation and evolve as quickly as RNA viruses. Although the recombination-prone nature of begomoviruses has been extensively demonstrated, the relative contribution of recombination and mutation to the genetic variation of begomovirus populations has not been assessed. We estimated the genetic variability of begomovirus datasets from around the world. An uneven distribution of genetic variation across the length of the cp and rep genes due to recombination was evident from our analyses. To estimate the relative contributions of recombination and mutation to the genetic variability of begomoviruses, we mapped all substitutions over maximum likelihood trees and counted the number of substitutions on branches which were associated with recombination (ηr) and mutation (ημ). In addition, we also estimated the per generation relative rates of both evolutionary mechanisms (r/μ) to express how frequently begomovirus genomes are affected by recombination relative to mutation. We observed that the composition of genetic variation in all begomovirus datasets was dominated by mutation. Additionally, the low correlation between the estimates indicated that the relative contributions of recombination and mutation are not necessarily a function of their relative rates. Our results show that, although a considerable fraction of the genetic variation levels could be assigned to recombination, it was always lower than that due to mutation, indicating that the diversification of begomovirus populations is predominantly driven by mutational dynamics.