Truly ubiquitous CRESS DNA viruses scattered across the eukaryotic tree of life
Truly ubiquitous CRESS DNA viruses scattered across the eukaryotic tree of life
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DOI：
10.1111/jeb.13927
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发表时间：
2021-09-23
影响因子：
2.1
通讯作者：
Duffy, Siobain
中科院分区：
文献类型：
--
作者：
Zhao, Lele;Lavington, Erik;Duffy, Siobain
直到最近，大多数检测到的病毒和特征都具有经济意义，与农业和医疗疾病有关。对于真核生物感染的环状Rep(复制相关蛋白)编码单链DNA(Cress DNA)的病毒来说，情况无疑是如此，它们被认为是相对较小的一组病毒。随着过去十年来元基因组测序的爆炸性增长和滚环复制用于序列扩增的越来越多的使用，科学家们已经识别和注释了大量的新的水芹DNA病毒-许多没有已知的宿主，但已经发现与真核生物有关的病毒。细胞基因组学的类似进展揭示了许多真核生物具有与病毒Rep同源的内源序列，这不仅为重建Cress DNA病毒的进化史提供了化石记录，而且还揭示了仅凭其序列就能揭示病毒的潜在宿主物种。Rep蛋白是一种保守的蛋白质，所有的水芹DNA病毒都利用它来帮助滚环复制，已知这种复制在少数真核物种(特别是烟草和水山药)中是内源性的。使用tBLASTn在GenBank的非冗余真核数据库中系统地搜索内源性Rep样序列。我们利用宽松的搜索标准在真核基因组中捕获整合的Rep序列，鉴定了93个独特的物种，它们的核、质粒(1个物种)、线粒体(6个物种)或叶绿体(8个物种)基因组中都有Rep的内源性片段。这些物种来自19个不同的门，分散在真核生命树上。外源和内源CRESS DNA病毒代表树拓扑结构表明，一个未知病毒家族的潜在宿主，并支持基因组病毒的主要真菌宿主范围。
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.