Dinucleotide Composition in Animal RNA Viruses Is Shaped More by Virus Family than by Host Species
Dinucleotide Composition in Animal RNA Viruses Is Shaped More by Virus Family than by Host Species
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DOI：
10.1128/jvi.02381-16
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发表时间：
2017-04-01
影响因子：
5.4
通讯作者：
Holmes, Edward C.
中科院分区：
文献类型：
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作者：
Di Giallonardo, Francesca;Schlub, Timothy E.;Holmes, Edward C.
病毒利用宿主的细胞机制进行复制。因此，有人提出病毒的核苷酸和二核苷酸组成应与其宿主物种的核苷酸和二核苷酸组成相匹配。如果这一点得到支持，那么就有可能使用二核苷酸组成来预测宏基因组调查中采样的病毒的真实宿主物种。然而，同样清楚的是，不同的病毒分类群往往具有独特的二核苷酸组成模式，这可能与宿主物种无关。为了确定宿主与病毒家族在形成二核苷酸组成方面的作用的相对强度，我们对来自15个宿主组的20个RNA病毒家族进行了比较分析，这些宿主组跨越两个动物门和900多种病毒物种。特别是，我们确定了16种可能的二核苷酸的比值比，并进行了判别分析，以评估病毒二核苷酸组合物的能力，以预测正确的病毒家族或宿主分类群，它是从分离。值得注意的是，虽然这里分析的数据中有81%被预测为正确的病毒家族，但这些数据中只有62%被预测为正确的亚门/纲宿主，只有32%被预测为正确的哺乳动物目的。类似地，二核苷酸组成对单个病毒家族内的不同宿主具有弱预测能力。因此，我们得出结论，二核苷酸组成一般是均匀的病毒家族内，但不太好地反映其宿主物种。这对于仅从病毒基因组序列准确预测宿主物种的尝试具有明显的意义。重要性确定病毒基因组的形成过程是理解病毒进化和出现的核心。一个特别重要的问题是为什么核苷酸和二核苷酸的频率在病毒之间有如此明显的差异。特别是，目前尚不清楚宿主物种或病毒家族对二核苷酸频率的影响最大，以及二核苷酸组成是否可以用于准确预测宿主物种。使用比较分析，我们表明，二核苷酸组合物具有很强的系统发育相关性，在不同的RNA病毒家族，这样的二核苷酸组合物可以预测的家庭，从该病毒序列已被分离。相反，二核苷酸组成对病毒家族内和不同病毒家族之间的不同宿主物种具有较差的预测能力，表明宿主对病毒基因组的二核苷酸组成具有相对较小的影响。
Viruses use the cellular machinery of their hosts for replication. It has therefore been proposed that the nucleotide and dinucleotide compositions of viruses should match those of their host species. If this is upheld, it may then be possible to use dinucleotide composition to predict the true host species of viruses sampled in metagenomic surveys. However, it is also clear that different taxonomic groups of viruses tend to have distinctive patterns of dinucleotide composition that may be independent of host species. To determine the relative strength of the effect of host versus virus family in shaping dinucleotide composition, we performed a comparative analysis of 20 RNA virus families from 15 host groupings, spanning two animal phyla and more than 900 virus species. In particular, we determined the odds ratios for the 16 possible dinucleotides and performed a discriminant analysis to evaluate the capability of virus dinucleotide composition to predict the correct virus family or host taxon from which it was isolated. Notably, while 81% of the data analyzed here were predicted to the correct virus family, only 62% of these data were predicted to their correct subphylum/class host and a mere 32% to their correct mammalian order. Similarly, dinucleotide composition has a weak predictive power for different hosts within individual virus families. We therefore conclude that dinucleotide composition is generally uniform within a virus family but less well reflects that of its host species. This has obvious implications for attempts to accurately predict host species from virus genome sequences alone.IMPORTANCE Determining the processes that shape virus genomes is central to understanding virus evolution and emergence. One question of particular importance is why nucleotide and dinucleotide frequencies differ so markedly between viruses. In particular, it is currently unclear whether host species or virus family has the biggest impact on dinucleotide frequencies and whether dinucleotide composition can be used to accurately predict host species. Using a comparative analysis, we show that dinucleotide composition has a strong phylogenetic association across different RNA virus families, such that dinucleotide composition can predict the family from which a virus sequence has been isolated. Conversely, dinucleotide composition has a poorer predictive power for the different host species within a virus family and across different virus families, indicating that the host has a relatively small impact on the dinucleotide composition of a virus genome.