Comprehensive analysis of recombinant viruses and the role of recombination

对世界上具有代表性的32个芜菁花叶病毒(TuMV)分离物的基因组进行了测序，并对这些分离物和以前报道的6个分离物进行了分析。至少五分之一的序列是重组的。在系统发育分析中，以日本山药花叶病毒基因组序列为外类群，未显示明显重组的TuMV序列形成一个单系统群，具有4个良好的谱系。这些类群与致病力和种源的差异相关；所有其他类群的姊妹群是欧亚非油菜属B株分离物，可能代表了TuMV的祖先种群，而该种群最近出现的分支可能是仅在东亚发现的BR株系分离物。8个分离株，全部来自东亚，是明确的重组体，很可能是最近重组事件的后代，而来自世界其他地区的类似数量的分离物，似乎是更老的重组体。Thi…通过对14 2个分离物的寄主范围和基因序列的比较，分析了欧亚大陆芜菁花叶病毒种群的遗传结构。从欧亚大陆西部采集的分离物主要侵染十字花科植物，而从东部欧亚大陆采集的分离物同时侵染油菜和萝卜属植物。对基因组4个区域(占全序列的1/3)的重组位点(RSS)的分析表明，在两个亚群中，P1基因的重组频率高于其他基因区域，但RSS位于亚群基因组的不同部分。对核苷酸多样性的估计表明，西欧亚亚种群比东欧亚亚种群更具多样性。这些亚群体似乎独立于欧洲祖先群体进化，它们的遗传结构可能反映了创始人效应。较少

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