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首页> 外文期刊>Journal of genetics >Molecular adaptation within the coat protein-encoding gene of Tunisian almond isolates of Prunus necrotic ringspot virus
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Molecular adaptation within the coat protein-encoding gene of Tunisian almond isolates of Prunus necrotic ringspot virus

机译：李属坏死环斑病毒突尼斯杏仁分离物外壳蛋白编码基因内的分子适应性

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摘要

The sequence alignments of five Tunisian isolates of Prunus necrotic ringspot virus (PNRSV) were searched for evidence of recombination and diversifying selection. Since failing to account for recombination can elevate the false positive error rate in positive selection inference, a genetic algorithm (GARD) was used first and led to the detection of potential recombination events in the coat protein-encoding gene of that virus. The Recco algorithm confirmed these results by identifying, additionally, the potential recombinants. For neutrality testing and evaluation of nucleotide polymorphism in PNRSV CP gene, Tajima's D, and Fu and Li's D and F statistical tests were used. About selection inference, eight algorithms (SLAC, FEL, IFEL, REL, FUBAR, MEME, PARRIS, and GA branch) incorporated in HyPhy package were utilized to assess the selection pressure exerted on the expression of PNRSV capsid. Inferred phylogenies pointed out, in addition to the three classical groups (PE-5, PV-32, and PV-96), the delineation of a fourth cluster having the new proposed designation SW6, and a fifth clade comprising four Tunisian PNRSV isolates which underwent recombination and selective pressure and to which the name Tunisian outgroup was allocated.
机译：寻找五个突尼斯坏死环斑病毒（PNRSV）突尼斯分离株的序列比对，以寻找重组和多样化选择的证据。由于无法考虑重组会提高阳性选择推断中的假阳性错误率，因此首先使用遗传算法（GARD），并导致检测到该病毒外壳蛋白编码基因中的潜在重组事件。 Recco算法通过另外鉴定潜在的重组体，证实了这些结果。为了进行PNRSV CP基因的中性测试和核苷酸多态性评估，使用了Tajima D和Fu and Li的D和F统计测试。关于选择推论，利用HyPhy程序包中包含的八个算法（SLAC，FEL，IFEL，REL，FUBAR，MEME，PARRIS和GA分支）来评估选择压力对PNRSV衣壳表达的影响。推断的系统发育学指出，除了三个经典组（PE-5，PV-32和PV-96）之外，还描绘了具有新提议名称SW6的第四个星团以及包含四个突尼斯PNRSV分离株的第五个进化枝。经历了重组和选择性压力，并因此获得了突尼斯小组的名字。

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