Low linkage disequilibrium indicative of recombination in foot-and-mouth disease virus gene sequence alignments
Low linkage disequilibrium indicative of recombination in foot-and-mouth disease virus gene sequence alignments
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DOI：
10.1099/vir.0.19588-0
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发表时间：
2004-05-01
影响因子：
3.8
通讯作者：
Awadalla, P
中科院分区：
文献类型：
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作者：
Haydon, DT;Bastos, ADS;Awadalla, P
对口蹄疫病毒（FMDV）进行了基因重组检测。我们的方法估计了对重组敏感的连锁不平衡（LID）的汇总统计量。利用家谱关系、速率异质性和突变参数，我们模拟了没有重组的匹配RNA序列数据集。这些模拟数据集允许在任何位点重复突变，以模拟病毒序列数据中的同源性，并允许在没有重组的情况下构建LID参数的零分布。我们通过两种方式测试重组：将观测数据中的LID与模拟数据中相应的零分布进行比较；并通过检测观察到的多态核苷酸位点对之间的LID与位点间距离之间的负相关关系。我们将这些测试应用于来自4种血清型的6个FMDV数据集，并在所有这些数据集中发现了一些重组的证据。
We have applied tests for detecting recombination to genes of foot-and-mouth disease virus (FMDV). Our approach estimated summary statistics of linkage disequilibrium (LID), which are sensitive to recombination. Using the genealogical relationships, rate heterogeneity and mutation parameters estimated from individual sets of aligned gene sequences, we simulated matching RNA sequence datasets without recombination. These simulated datasets allowed for recurrent mutations at any site to mimic homoplasy in virus sequence data and allow construction of null distributions for LID parameters expected in the absence of recombination. We tested for recombination in two ways: by comparing LID in observed data with corresponding null distributions obtained from simulated data; and by testing for a negative relationship between observed LID between pairs of polymorphic nucleotide sites and inter-site distance. We applied these tests to six FMDV datasets from four serotypes and found some evidence for recombination in all of them.