Marsupial viruses are understudied compared to their eutherian mammal counterparts, although they may pose severe threats to vulnerable marsupial populations. Genomic viral integrations, termed ‘endogenous viral elements’ (EVEs), could protect the host from infection. It is widely known past viral infections and EVEs play an active role in antiviral defence in invertebrates and plants. This study aimed to characterise actively transcribed EVEs in Australian marsupial species, because they may play an integral role in cellular defence against viruses. This study screened publicly available RNA sequencing data sets (n = 35) and characterised 200 viral transcripts from thirteen Australian marsupial species. Of the 200 transcripts, 188 originated from either Bornaviridae, Filoviridae, or Parvoviridae EVEs. The other twelve transcripts were from putative active infections from members of the Herpesviridae and Anelloviridae, and Hepadnaviridae. EVE transcripts (n = 188) were mapped to marsupial genomes (where available, n = 5/13) to identify the genomic insertion sites. Of the 188 transcripts, 117 mapped to 39 EVEs within the koala, bare-nosed wombat, tammar wallaby, brushtail possum, and Tasmanian devil genomes. The remaining eight animals had no available genome (transcripts n = 71). Every marsupial has Bornaviridae, Filoviridae, and Parvoviridae EVEs, a trend widely observed in eutherian mammals. Whilst eutherian bornavirus EVEs are predominantly nucleoprotein-derived, marsupial bornavirus EVEs demonstrate a surprising replicase gene bias. We predicted these widely distributed EVEs were conserved within marsupials from ancient germline integrations, as many were over 65 million years old. One bornavirus replicase EVE, present in six marsupial genomes, was estimated to be 160 million years old, predating the American–Australian marsupial split. We considered transcription of these EVEs through small non-coding RNA as an ancient viral defence. Consistent with this, in koala small RNA sequence data sets, we detected Bornaviridae replicase and Filoviridae nucleoprotein produced small RNA. These were enriched in testis tissue, suggesting they could protect marsupials from vertically transmitted viral integrations.

中文翻译：

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有袋动物中的古代病毒整合：一种潜在的抗病毒防御

与真兽哺乳动物病毒相比，有袋动物病毒的研究不足，尽管它们可能对脆弱的有袋动物种群构成严重威胁。基因组病毒整合，称为“内源性病毒元件”(EVE)，可以保护宿主免受感染。众所周知，过去的病毒感染和 EVE 在无脊椎动物和植物的抗病毒防御中发挥着积极作用。本研究旨在表征澳大利亚有袋动物中活跃转录的 EVE，因为它们可能在细胞防御病毒中发挥不可或缺的作用。这项研究筛选了公开可用的 RNA 测序数据集 (n = 35)，并对来自 13 种澳大利亚有袋动物的 200 种病毒转录本进行了表征。在 200 个转录本中，188 个来自博尔病毒科、丝状病毒科或细小病毒科 EVE。其他 12 个转录本来自推定的活跃感染，来自疱疹病毒科和指环病毒科以及嗜肝病毒科的成员。EVE 转录本 (n = 188) 被映射到有袋动物基因组（如果可用，n = 5/13）以识别基因组插入位点。在 188 个转录本中，117 个映射到考拉、裸鼻袋熊、袋鼠、刷尾负鼠和袋獾基因组中的 39 个 EVE。其余八只动物没有可用的基因组（转录本 n = 71）。每个有袋动物都有博尔病毒科、丝状病毒科和细小病毒科 EVE，这是一种在真兽类哺乳动物中广泛观察到的趋势。虽然真兽类博尔纳病毒 EVE 主要是核蛋白衍生的，但有袋类博尔纳病毒 EVE 表现出令人惊讶的复制酶基因偏倚。我们预测这些广泛分布的 EVEs 在有袋类动物中是从古代种系整合中保存下来的，因为许多有袋类动物的年龄超过 6500 万年。一种存在于六个有袋动物基因组中的博尔纳病毒复制酶 EVE 据估计已有 1.6 亿年历史，早于美洲-澳大利亚有袋动物分裂。我们认为通过小的非编码 RNA 转录这些 EVE 是一种古老的病毒防御。与此一致，在考拉小RNA序列数据集中，我们检测到博尔病毒科复制酶和丝状病毒科核蛋白产生的小RNA。它们富含睾丸组织，表明它们可以保护有袋动物免受垂直传播的病毒整合。早于美国-澳大利亚有袋动物分裂。我们认为通过小的非编码 RNA 转录这些 EVE 是一种古老的病毒防御。与此一致，在考拉小RNA序列数据集中，我们检测到博尔病毒科复制酶和丝状病毒科核蛋白产生的小RNA。它们富含睾丸组织，表明它们可以保护有袋动物免受垂直传播的病毒整合。早于美国-澳大利亚有袋动物分裂。我们认为通过小的非编码 RNA 转录这些 EVE 是一种古老的病毒防御。与此一致，在考拉小RNA序列数据集中，我们检测到博尔病毒科复制酶和丝状病毒科核蛋白产生的小RNA。它们富含睾丸组织，表明它们可以保护有袋动物免受垂直传播的病毒整合。