Abstract Papillomaviruses (PVs) have evolved through a complex evolutionary scenario where virus–host co-evolution alone is not enough to explain the phenotypic and genotypic PV diversity observed today. Other evolutionary processes, such as host switch and recombination, also appear to play an important role in PV evolution. In this study, we have examined the genomic impact of a recombination event between distantly related PVs infecting Cetartiodactyla (even-toed ungulates and cetaceans). Our phylogenetic analyses suggest that one single recombination was responsible for the generation of extant ‘chimeric’ PV genomes infecting cetaceans. By correlating the phylogenetic relationships to the genomic content, we observed important differences between the recombinant and non-recombinant cetartiodactyle PV genomes. Notably, recombinant PVs contain a unique set of conserved motifs in the upstream regulatory region (URR). We interpret these regulatory changes as an adaptive response to drastic changes in the PV genome. In terms of codon usage preferences (CUPrefs), we did not detect any particular differences between orthologous open reading frames in recombinant and non-recombinant PVs. Instead, our results are in line with previous observations suggesting that CUPrefs in PVs are rather linked to gene expression patterns as well as to gene function. We show that the non-coding URR of PVs infecting cetaceans, the central regulatory element in these viruses, exhibits signs of adaptation following a recombination event. Our results suggest that also in PVs, the evolution of gene regulation can play an important role in speciation and adaptation to novel environments.

中文翻译：

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感染鲸类动物的乳头瘤病毒在重组事件后表现出基因组适应的迹象

摘要 乳头瘤病毒 (PV) 是通过复杂的进化场景进化而来的，在这种场景中，仅病毒-宿主共同进化不足以解释当今观察到的表型和基因型 PV 多样性。其他进化过程，如宿主转换和重组，似乎也在光伏进化中发挥重要作用。在这项研究中，我们检查了远亲 PVs 感染 Cetartiodactyla（偶趾有蹄类动物和鲸目动物）之间重组事件的基因组影响。我们的系统发育分析表明，一个单一的重组负责产生感染鲸类动物的现存“嵌合”PV 基因组。通过将系统发育关系与基因组含量相关联，我们观察到重组和非重组鲸豚类 PV 基因组之间的重要差异。尤其，重组 PV 在上游调控区 (URR) 中包含一组独特的保守基序。我们将这些监管变化解释为对 PV 基因组急剧变化的适应性反应。在密码子使用偏好 (CUPrefs) 方面，我们没有检测到重组和非重组 PV 中直系同源开放阅读框之间的任何特定差异。相反，我们的结果与之前的观察结果一致，表明 PV 中的 CUPrefs 与基因表达模式以及基因功能相当相关。我们表明，感染鲸类动物的 PV 的非编码 URR，这些病毒的中心调控元件，在重组事件后表现出适应的迹象。我们的结果表明，同样在 PVs 中，基因调控的进化可以在物种形成和适应新环境中发挥重要作用。