Comprehensive analysis of recombinant viruses and the role of recombination

一个代表性的全球收集的32芜菁花叶病毒（TuMV）分离株的基因组进行了测序，这些，连同6个以前报道的，进行了分析。至少五分之一的序列是重组的。在系统发育分析中，使用日本山药花叶病毒的基因组序列作为外群，TuMV序列，没有表现出明确的重组形成了一个单系组，有四个良好的支持谱系。这些分组相关的致病性和种源的差异，所有其他的姐妹组是欧亚B株分离的非芸苔属，可能代表祖先TuMV人口，和最近出现的人口的分支可能是BR株分离株只在东亚发现。8个分离株，都来自东亚，明确的重组，可能是最近的重组事件的后代，而类似的数字，从世界其他地区，似乎是旧的重组。Thi 关于我们 通过对欧亚地区芜菁花叶病毒142个分离物的寄主范围和基因序列的比较，对芜菁花叶病毒欧亚地区各分离物的遗传结构进行了分析。大多数分离物收集在欧亚大陆西部感染芸苔属植物，而那些从欧亚大陆东部感染芸苔属和萝卜属植物。在基因组的四个区域（全序列的三分之一）的重组位点（RS）的分析表明，P1基因的重组频率比其他基因区域在两个亚群，但RS位于不同的部分的亚群的基因组。核苷酸多样性的估计表明，西欧亚亚群比东欧亚亚群更多样化。这些亚种群似乎是独立于祖先欧洲种群进化而来的，它们的遗传结构可能反映了创始人效应。少

The genomes of a representative worldwide collection of thirty-two Turnip mosaic virus(TuMV) isolates were sequenced and these, together with six previously reported, were analysed. At least one fifth of the sequences were recombinant. In phylogenetic analyses, using genomic sequences of Japanese yam mosaic virus as an outgroup, the TuMV sequences that did not show clear recombination formed a monophyletic group with four well-supported lineages. These groupings correlated with differences in pathogenicity and provenance ; the sister group to all others was of Eurasian B-strain isolates from non-brassicas, and probably represents the ancestral TuMV population, and the most recently ‘emerged' branch of the population was probably that of BR-strain isolates found only in east Asia. Eight isolates, all from east Asia, were clear recombinants, probably the progeny of recent recombination events, whereas a similar number, from other parts of the world, were seemingly older recombinants. Thi … More s difference indicates that the presence of clear recombinants in a sub-population may be a molecular signature of a recent ‘emergence'.The genetic structure of populations of Turnip mosaic virus in Eurasia was assessed by making host range and gene sequence comparisons of 142 isolates. Most isolates collected in west Eurasia infected Brassica plants whereas those from east Eurasia infected both Brassica and Raphanus plants. Analyses of recombination sites(RSs) in four regions of the genome (one third of the full sequence), showed that the P1 gene had recombined more frequently than the other gene regions in both sub-populations, but that the RSs were located in different parts of the genomes of the sub-populations. Estimates of nucleotide diversity showed that the west Eurasian sub-population was more diverse than the east Eurasian sub-population. These sub-populations seem to have evolved independently from the ancestral European population, and their genetic structure probably reflects founder effects. Less