Comprehensive analysis of recombinant viruses and the role of recombination

对世界范围内具有代表性的32株萝卜花叶病毒（TuMV）分离株的基因组进行了测序，并对这些分离株与先前报道的6株分离株进行了分析。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的基因组序列为外群，未显示明显重组的TuMV序列形成了一个单系群，具有四个良好支持的谱系。这些分组与致病性和种源的差异相关；与所有其他类群的姊妹类群是来自非芸苔属植物的欧亚b株分离株，可能代表祖先TuMV种群，而最近“出现”的种群分支可能是仅在东亚发现的br株分离株。来自东亚的8个分离株是明显的重组株，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株似乎是更古老的重组株。这种差异表明，在一个亚种群中存在明显的重组可能是最近“出现”的分子特征。通过对欧亚地区萝卜花叶病毒142个分离株的寄主范围和基因序列的比较，对欧亚地区萝卜花叶病毒居群的遗传结构进行了评价。大部分来自欧亚大陆西部的分离株感染了芸苔属植物，而来自欧亚大陆东部的分离株同时感染了芸苔属和莴苣属植物。对基因组四个区域（全序列的三分之一）的重组位点（RSs）分析表明，P1基因在两个亚群体中重组频率高于其他基因区域，但这些重组位点位于亚群体基因组的不同部位。对核苷酸多样性的估计表明，欧亚西部亚群比欧亚东部亚群更具多样性。这些亚种群似乎是独立于祖先欧洲种群进化而来的，他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