Statistical Analysis on Detecting Recombination Sites in DNA-β Satellites Associated with Old World Geminiviruses.
Statistical Analysis on Detecting Recombination Sites in DNA-β Satellites Associated with Old World Geminiviruses.
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DOI：
10.3389/fpsyt.2010.00138
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发表时间：
2010
影响因子：
4.7
通讯作者：
Yoshida R
中科院分区：
文献类型：
--
作者：
Xu K;Yoshida R
虽然通过重组交换遗传信息在病毒进化中起着重要作用，但尚不清楚它如何产生多样性。了解重组事件有助于研究新病毒株或新病毒的进化。双生病毒是一类具有双义单链环状DNA基因组的植物病毒，是农业生产中最重要的经济植物病毒之一。最近发现小的环状单链DNA卫星，称为DNA-β，与一些双生病毒感染有关。在本文中，我们分析了几个双生病毒的DNA-β序列的重组事件，使用系统发育和统计分析，我们发现一个菌株ToLCMaB具有重组模式，是一个重组分子之间的两个菌株从两个物种，PaLCuB-[IN：Chi：05]（主要的父母）和ToLCB-[IN：CP：04]（次要的父母）。我们建议，这一重组事件有助于在印度南部的ToLCMaB菌株的演变。Webb等人提出的隐马尔可夫链（Hidden Markov Chain，HMM）方法通过整个序列比对来估计系统发育树，为我们提供了这些DNA-β菌株的重组历史。首次将该统计方法应用于DNA-β重组的研究，给出了DNA-β重组的清晰的重组历史。
Although exchange of genetic information by recombination plays an important role in the evolution of viruses, it is not clear how it generates diversity. Understanding recombination events helps with the study of the evolution of new virus strains or new viruses. Geminiviruses are plant viruses which have ambisense single-stranded circular DNA genomes and are one of the most economically important plant viruses in agricultural production. Small circular single-stranded DNA satellites, termed DNA-β, have recently been found to be associated with some geminivirus infections. In this paper we analyze several DNA-β sequences of geminiviruses for recombination events using phylogenetic and statistical analysis and we find that one strain from ToLCMaB has a recombination pattern and is a recombinant molecule between two strains from two species, PaLCuB-[IN:Chi:05] (major parent) and ToLCB-[IN:CP:04] (minor parent). We propose that this recombination event contributed to the evolution of the strain of ToLCMaB in South India. The Hidden Markov Chain (HMM) method developed by Webb et al. estimating phylogenetic tree through out the whole alignment provide us a recombination history of these DNA-β strains. It is the first time that this statistic method has been used on DNA-β recombination study and give a clear recombination history of DNA-β recombination.