Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination
Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination
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DOI：
10.1099/vir.0.82335-0
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发表时间：
2007-01-01
影响因子：
3.8
通讯作者：
Gibbs, Adrian J.
中科院分区：
文献类型：
--
作者：
Ohshima, Kazusato;Tomitaka, Yasuhiro;Gibbs, Adrian J.
马铃薯Y病毒具有可变的单链RNA基因组，并且许多病毒显示出明显的重组证据。本报告研究了92株马铃薯Y病毒属芜菁花叶病毒（TuMV）基因组中重组位点的分布; 42株来自国际基因序列数据库，另外50株来自欧洲和亚洲的田间样品。使用7种不同的序列比较方法检查序列中重组的证据，并通过序列组成分析确认每个位点的确切位置。除了小的6 K1蛋白基因外，在整个基因组中都发现了重组位点，只有24个基因组（26个没有重组的证据）。在Pi基因和Cl/6 K2/VPg基因区域中发现了统计学显著的重组位点簇。大多数重组位点由相似长度的富含GC序列的上游（5 '）区域和富含AU序列的下游（3'）区域邻接。重组位点的存在和类型与种源，宿主类型和系统发育关系之间的相关性进行了讨论，重组在TuMV进化中的作用。
Potyviruses have variable single-stranded RNA genomes and many show clear evidence of recombination. This report studied the distribution of recombination sites in the genomes of 92 isolates of the potyvirus Turnip mosaic virus (TuMV); 42 came from the international gene sequence databases and an additional 50 complete genomic sequences were generated from field samples collected in Europe and Asia. The sequences were examined for evidence of recombination using seven different, sequence comparison methods and the exact position of each site was confirmed by sequence composition analysis. Recombination sites were found throughout the genomes, except in the small 6K1 protein gene, and only 24 of the genomes (26 showed no evidence of recombination. Statistically significant clusters of recombination sites were found in the Pi gene and in the Cl/6K2/VPg gene region. Most recombination sites were bordered by an upstream (5') region of GC-rich and downstream (3') region of AU-rich sequence of a similar length. Correlations between the presence and type of recombination site and provenance, host type and phylogenetic relationships are discussed, as is the role of recombination in TuMV evolution.