Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus Tomato yellow leaf curl virus
Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus Tomato yellow leaf curl virus
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DOI：
10.1128/jvi.01929-07
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发表时间：
2008-01-01
影响因子：
5.4
通讯作者：
Holmes, Edward C.
中科院分区：
文献类型：
--
作者：
Duffy, Siobain;Holmes, Edward C.
双生病毒属是一种具有单链DNA（ssDNA）基因组的植物毁灭性病毒。尽管这类植物病原体的重要性，有没有估计的核苷酸取代率的双生病毒。我们在这里报告的进化速率的番茄黄化曲叶病引起的病毒，一个深入研究组的单分Begomoviruses。使用贝叶斯结合方法分析了1988年至2006年间从患病植物中分离的来自GenBank的序列。平均基因组替换率估计为2.88 × 10（-4）个核苷酸替换/位点/年（subs/site/year），尽管该速率可能被番茄黄化曲叶病毒基因组内的频繁重组所混淆。包含分离的外壳蛋白（V1）基因的无重组体数据集产生了类似的平均速率（4.63 × 10（-4）subs/site/year），验证了蛋白质编码区基因组替换速率的数量级。基因间区，这是已知的更可变的，被发现进化得更快，与类似的平均替换率为1.56 × 10（-3）次/地点/年。值得注意的是，这些取代率，第一次报告的植物DNA病毒，是在与哺乳动物ssDNA病毒和RNA病毒先前估计。因此，我们的研究结果表明，双生病毒的高进化率并不主要是由于频繁的重组，并可能解释他们的能力，出现在新的主机。
Geminiviruses are devastating viruses of plants that possess single-stranded DNA (ssDNA) DNA genomes. Despite the importance of this class of phytopathogen, there have been no estimates of the rate of nucleotide substitution in the geminiviruses. We report here the evolutionary rate of the tomato yellow leaf curl disease-causing viruses, an intensively studied group of monopartite begomoviruses. Sequences from GenBank, isolated from diseased plants between 1988 and 2006, were analyzed using Bayesian coalescent methods. The mean genomic substitution rate was estimated to be 2.88 X 10(-4) nucleotide substitutions per site per year (subs/site/year), although this rate could be confounded by frequent recombination within Tomato yellow leaf curl virus genomes. A recombinant-free data set comprising the coat protein (V1) gene in isolation yielded a similar mean rate (4.63 X 10(-4) subs/site/year), validating the order of magnitude of genomic substitution rate for protein-coding regions. The intergenic region, which is known to be more variable, was found to evolve even more rapidly, with a mean substitution rate of similar to 1.56 X 10(-3) subs/site/year. Notably, these substitution rates, the first reported for a plant DNA virus, are in line with those estimated previously for mammalian ssDNA viruses and RNA viruses. Our results therefore suggest that the high evolutionary rate of the geminiviruses is not primarily due to frequent recombination and may explain their ability to emerge in novel hosts.