Abstract The family Geminiviridae contains viruses with single-stranded DNA genomes that have been found infecting a wide variety of angiosperm species. The discovery within the last 25 years of endogenous geminivirus-like (EGV) elements within the nuclear genomes of several angiosperms has raised questions relating to the pervasiveness of EGVs and their impacts on host biology. Only a few EGVs have currently been characterized and it remains unclear whether any of these have influenced, or are currently influencing, the evolutionary fitness of their hosts. We therefore undertook a large-scale search for evidence of EGVs within 134 genome and 797 transcriptome sequences of green plant species. We detected homologues of geminivirus replication-associated protein (Rep) genes in forty-two angiosperm species, including two monocots, thirty-nine dicots, and one ANITA-grade basal angiosperm species (Amborella trichopoda). While EGVs were present in the members of many different plant orders, they were particularly common within the large and diverse order, Ericales, with the highest copy numbers of EGVs being found in two varieties of tea plant (Camellia sinensis). Phylogenetic and clustering analyses revealed multiple highly divergent previously unknown geminivirus Rep lineages, two of which occur in C.sinensis alone. We find that some of the Camellia EGVs are likely transcriptionally active, sometimes co-transcribed with the same host genes across several Camellia species. Overall, our analyses expand the known breadths of both geminivirus diversity and geminivirus host ranges, and strengthens support for the hypothesis that EGVs impact the biology of their hosts.

中文翻译：

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大规模调查揭示了植物内源性双生病毒序列的普遍性和潜在功能

摘要 Geminiviridae 家族包含具有单链 DNA 基因组的病毒，已发现这些病毒可感染多种被子植物物种。在过去的 25 年里，在几种被子植物的核基因组中发现了内源性双生病毒样 (EGV) 元件，这引发了与 EGV 的普遍性及其对宿主生物学影响有关的问题。目前仅对少数 EGV 进行了表征，尚不清楚这些 EGV 中是否有任何影响或目前正在影响其宿主的进化适应性。因此，我们在绿色植物物种的 134 个基因组和 797 个转录组序列中对 EGV 的证据进行了大规模搜索。我们在 42 种被子植物中检测到双生病毒复制相关蛋白 (Rep) 基因的同源物，包括两种单子叶植物、39 种双子叶植物、和一种 ANITA 级基础被子植物（Amborella trichopoda）。虽然 EGV 存在于许多不同植物目的成员中，但它们在大而多样的目 Ericales 中特别常见，在两个品种的茶树（Camellia sinensis）中发现的 EGV 拷贝数最高。系统发育和聚类分析揭示了多个高度发散的先前未知的双生病毒 Rep 谱系，其中两个仅发生在 C.sinensis 中。我们发现一些山茶 EGV 可能具有转录活性，有时与几个山茶属物种的相同宿主基因共转录。总的来说，我们的分析扩大了双生病毒多样性和双生病毒宿主范围的已知广度，并加强了对 EGV 影响其宿主生物学的假设的支持。