BACKGROUND Virophages are small viruses with double-stranded DNA genomes that replicate along with giant viruses and co-infect eukaryotic cells. Due to the paucity of virophage reference genomes, a collective understanding of the global virophage diversity, distribution, and evolution is lacking. RESULTS Here we screened a public collection of over 14,000 metagenomes using the virophage-specific major capsid protein (MCP) as "bait." We identified 44,221 assembled virophage sequences, of which 328 represent high-quality (complete or near-complete) genomes from diverse habitats including the human gut, plant rhizosphere, and terrestrial subsurface. Comparative genomic analysis confirmed the presence of four core genes in a conserved block. We used these genes to establish a revised virophage classification including 27 clades with consistent genome length, gene content, and habitat distribution. Moreover, for eight high-quality virophage genomes, we computationally predicted putative eukaryotic virus hosts. CONCLUSION Overall, our approach has increased the number of known virophage genomes by 10-fold and revealed patterns of genome evolution and global virophage distribution. We anticipate that the expanded diversity presented here will provide the backbone for further virophage studies.

中文翻译：

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通过全球宏基因组学发现了病毒体的多样性，进化和分类。

背景技术噬菌体是具有双链DNA基因组的小型病毒，可​​与巨型病毒一起复制并共同感染真核细胞。由于缺乏噬菌体参考基因组，因此缺乏对全球噬菌体多样性，分布和进化的集体理解。结果在这里，我们使用病毒体特异性主要衣壳蛋白（MCP）作为“诱饵”，筛选了超过14,000个基因组的公开集合。我们确定了44,221个组装的噬菌体序列，其中328个代表了来自不同栖息地的高质量（完整或接近完整）基因组，包括人类肠道，植物根际和陆地地下。比较基因组分析证实了在保守的区块中存在四个核心基因。我们使用这些基因建立了修订后的食道分类，包括27个进化枝，具有一致的基因组长度，基因含量和栖息地分布。此外，对于八个高质量的噬菌体基因组，我们在计算上预测了推定的真核病毒宿主。结论总体而言，我们的方法将已知的噬菌体基因组数目增加了10倍，并揭示了基因组进化和全球噬菌体分布的模式。我们预计，此处介绍的扩展多样性将为进一步的噬菌体研究提供基础。我们的方法将已知的噬菌体基因组数量增加了10倍，并揭示了基因组进化和全球噬菌体分布的模式。我们预计，此处介绍的扩展多样性将为进一步的噬菌体研究提供基础。我们的方法将已知的噬菌体基因组数量增加了10倍，并揭示了基因组进化和全球噬菌体分布的模式。我们预计，此处介绍的扩展多样性将为进一步的噬菌体研究提供基础。