Archaeal pleomorphic viruses belonging to the Pleolipoviridae family represent an enigmatic group as they exhibit unique genomic features and are thought to have evolved through recombination with different archaeal plasmids. However, most of our understanding of the diversity and evolutionary trajectories of this clade comes from a handful of isolated representatives. Here we present 164 new genomes of pleolipoviruses obtained from metagenomic data of Australian hypersaline lakes and publicly available metagenomic data. We perform a comprehensive analysis on the diversity and evolutionary relationships of the newly discovered viruses and previously described pleolipoviruses. We propose to classify the viruses into five genera within the Pleolipoviridae family, with one new genus represented only by virus genomes retrieved in this study. Our data support the current hypothesis that pleolipoviruses reshaped their genomes through recombining with multiple different groups of plasmids, which is reflected in the diversity of their predicted replication strategies. We show that the proposed genus Epsilonpleolipovirus has evolutionary ties to pRN1-like plasmids from Sulfolobus, suggesting that this group could be infecting other archaeal phyla. Interestingly, we observed that the genome size of pleolipoviruses is correlated to the presence or absence of an integrase. Analyses of the host range revealed that all but one virus exhibit an extremely narrow range, and we show that the predicted tertiary structure of the spike protein is strongly associated with the host family, suggesting a specific adaptation to the host S-layer glycoprotein organization.

中文翻译：

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重新审视多脂病毒科的进化轨迹和组织。

属于多脂病毒科的古菌多形性病毒是一个神秘的群体，因为它们表现出独特的基因组特征，并且被认为是通过与不同古菌质粒重组而进化的。然而，我们对这个分支的多样性和进化轨迹的大部分理解都来自少数孤立的代表。在这里，我们展示了从澳大利亚高盐湖泊的宏基因组数据和公开的宏基因组数据中获得的 164 个新的多脂病毒基因组。我们对新发现的病毒和先前描述的多脂病毒的多样性和进化关系进行了全面分析。我们建议将病毒分为多脂病毒科内的五个属，其中一个新属仅由本研究中检索到的病毒​​基因组代表。我们的数据支持当前的假设，即多脂病毒通过与多个不同组的质粒重组来重塑其基因组，这反映在其预测的复制策略的多样性上。我们表明，所提出的 Epsilonpleolipovirus 属与来自硫化叶菌属的 pRN1 样质粒具有进化联系，表明该群体可能感染其他古菌门。有趣的是，我们观察到多脂病毒的基因组大小与整合酶的存在或不存在相关。对宿主范围的分析表明，除一种病毒外，所有病毒都表现出极其狭窄的范围，并且我们表明，预测的刺突蛋白三级结构与宿主家族密切相关，表明对宿主 S 层糖蛋白组织的特定适应。