Until recently, most viruses detected and characterized were of economic significance, associated with agricultural and medical diseases. This was certainly true for the eukaryote-infecting circular Rep (replication-associated protein)-encoding single-stranded DNA (CRESS DNA) viruses, which were thought to be a relatively small group of viruses. With the explosion of metagenomic sequencing over the past decade and increasing use of rolling-circle replication for sequence amplification, scientists have identified and annotated copious numbers of novel CRESS DNA viruses - many without known hosts but which have been found in association with eukaryotes. Similar advances in cellular genomics have revealed that many eukaryotes have endogenous sequences homologous to viral Reps, which not only provide 'fossil records' to reconstruct the evolutionary history of CRESS DNA viruses but also reveal potential host species for viruses known by their sequences alone. The Rep protein is a conserved protein that all CRESS DNA viruses use to assist rolling-circle replication that is known to be endogenized in a few eukaryotic species (notably tobacco and water yam). A systematic search for endogenous Rep-like sequences in GenBank's non-redundant eukaryotic database was performed using tBLASTn. We utilized relaxed search criteria for the capture of integrated Rep sequence within eukaryotic genomes, identifying 93 unique species with an endogenized fragment of Rep in their nuclear, plasmid (one species), mitochondrial (six species) or chloroplast (eight species) genomes. These species come from 19 different phyla, scattered across the eukaryotic tree of life. Exogenous and endogenous CRESS DNA viral Rep tree topology suggested potential hosts for one family of uncharacterized viruses and supports a primarily fungal host range for genomoviruses.

中文翻译：

---

真正无处不在的 CRESS DNA 病毒散布在真核生命树中。

直到最近，大多数检测和表征的病毒都具有经济意义，与农业和医学疾病有关。对于感染真核生物的环状 Rep（复制相关蛋白）编码单链 DNA (CRESS DNA) 病毒来说，这当然是正确的，它们被认为是一个相对较小的病毒群。随着过去十年宏基因组测序的爆炸式增长以及越来越多地使用滚环复制进行序列扩增，科学家们已经鉴定并注释了大量新型 CRESS DNA 病毒——许多没有已知宿主，但已发现与真核生物有关。细胞基因组学的类似进展表明，许多真核生物具有与病毒 Reps 同源的内源序列，这不仅提供了“化石记录” 重建 CRESS DNA 病毒的进化历史，但也揭示了仅通过其序列已知的病毒的潜在宿主物种。Rep 蛋白是一种保守蛋白，所有 CRESS DNA 病毒都使用它来辅助滚环复制，已知这种蛋白在少数真核物种（特别是烟草和水山药）中内源化。使用 tBLASTn 在 GenBank 的非冗余真核数据库中系统搜索内源性 Rep 样序列。我们利用宽松的搜索标准来捕获真核基因组内的整合 Rep 序列，在其核、质粒（一种）、线粒体（六种）或叶绿体（八种）基因组中鉴定了 93 种具有内源化 Rep 片段的独特物种。这些物种来自 19 个不同的门，分散在真核生命树中。