ssRNA viruses from biotrophic Oomycetes form a new phylogenetic group between Nodaviridae and Tombusviridae

It is hard to overemphasize the role that metagenomics has had on our recent understanding of RNA virus diversity. Metagenomics in the 21st century has brought with it an explosion in the number of RNA virus species, genera, and families far exceeding that following the discovery of the microscope in the 18th century for eukaryotic life or culture media in the 19th century for bacteriology or the 20th century for virology. When the definition of success in organism discovery is measured by sequence diversity and evolutionary distance, RNA viruses win. This review explores the history of RNA virus metagenomics, reasons for the successes so far in RNA virus metagenomics, and methodological concerns. In addition, the review briefly covers clinical metagenomics and environmental metagenomics and highlights some of the critical accomplishments that have defined the fast pace of RNA virus discoveries in recent years. Slightly more than a decade in, the field is exhausted from its discoveries but knows that there is yet even more out there to be found.

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“…Tombusviridae and Nodaviridae? Tombunodavirus (Grasse and Spring, 2017;Greninger and DeRisi, 2015d).…”

Section: Pity the Ictvmentioning

confidence: 99%

A decade of RNA virus metagenomics is (not) enough

2018

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“…Knowledge on viruses infecting oomycetes is relatively limited (Sutela et al, 2019). Several viruses have been described in downy mildews (biotrophic plant parasites) including unclassified (+) ssRNA viruses on Sclerophthora macrospora with similarities to a Noda-Tombus-like virus (Yokoi et al, 2003) and in Plasmopara parasitica, which causes hypovirulence on its host (Grasse et al, 2013;Grasse and Spring, 2017). The genus Pythium is comprised of water and soilborne oomycetes causing moderate to significant damages in plant roots (Sutela et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Marine Oomycetes of the Genus Halophytophthora Harbor Viruses Related to Bunyaviruses

et al. 2020

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We investigated the incidence of RNA viruses in a collection of Halophytophthora spp. from estuarine ecosystems in southern Portugal. The first approach to detect the presence of viruses was based on the occurrence of dsRNA, typically considered as a viral molecule in plants and fungi. Two dsRNA-banding patterns (∼7 and 9 kb) were observed in seven of 73 Halophytophthora isolates tested (9.6%). Consequently, two dsRNA-hosting isolates were chosen to perform stranded RNA sequencing for de novo virus sequence assembly. A total of eight putative novel virus species with genomic affinities to members of the order Bunyavirales were detected and their full-length RdRp gene characterized by RACE. Based on the direct partial amplification of their RdRp gene by RT-PCR multiple viral infections occur in both isolates selected. Likewise, the screening of those viruses in the whole collection of Halophytophthora isolates showed that their occurrence is limited to one single Halophytophthora species. To our knowledge, this is the first report demonstrating the presence of negative (−) ssRNA viruses in marine oomycetes.

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“…However, using BLASTp, CruV-523 showed similarity to other RNA viruses with an e-value < 1e-9, which were not included in the analysis. The CP sequence similarity network analysis demonstrates the apparent homology of the CPs in our dataset with the CP of RNA viruses; specifically to unclassified RNA viruses that have RdRPs similar to either tombusviruses -also described as tombus-like viruses (77,91,92)-or to nodaviruses. The latter RNA viruses are proposed to belong to a chimeric group of viruses named tombunodaviruses (93).…”

Section: Crucivirus Cps Share Higher Genetic Identity Than Their Rep mentioning

confidence: 80%

“…contain the most similar capsid sequences to cruciviral capsids (15,27)-also have multipartite genomes (77). Unfortunately, no reliable method yet exists to match different sequences belonging to the same multisegmented virus in metagenomes, (76).…”

Section: Plasmopara Halstedii Virus a And Schlerophthora Macrospora Vmentioning

confidence: 99%

“…Additionally, the CP of cruciviruses, a suggested determinant of tropism (95,96), is homologous to the capsid of RNA viruses known to infect eukaryotes. The RNA viruses with a known host with capsids most similar to cruciviral capsids (tombunodaviruses) infect oomycetes, a group of filamentous eukaryotic stramenopiles (77).…”

Section: Members Of the Sar Supergroup Are Potential Crucivirus Hostsmentioning

confidence: 99%

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Unveiling Crucivirus Diversity by Mining Metagenomic Data

Higuera

Kasun

Torrance

et al. 2020

Preprint

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The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding ssDNA (CRESS-DNA) viruses that encode capsid proteins (CPs) that are most closely related to those encoded by RNA viruses in the family Tombusviridae. The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of CP genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and ten CP-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode.Most of the variation is reflected in the replication associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins, and that the exchange of Rep protein domains between cruciviruses is rarer than gene exchange. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses. IMPORTANCEViruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and are viruses that appear to have multiple origins from prokaryotic plasmids. CRESS-DNA viruses such as the cruciviruses, have homologues of capsid proteins (CPs) encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability. Bootstrap support 0.95 -1 0.8 -0.95 1 subs/site UF Bootstrap support 0.95 -1 0.8 -0.95 1 subs/site Rep CP A B * Endonuclease Helicase UF Bootstrap support 0.95 -1 0.8 -0.95 Cp-based clusters Endonuclease Helicase UF Bootstrap support 0.95 -1 0.8 -0.95 Endonuclease Helicase UF Bootstrap support 0.95 -1 0.8 -0.95

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ssRNA viruses from biotrophic Oomycetes form a new phylogenetic group between Nodaviridae and Tombusviridae

Cited by 12 publications

References 18 publications

A decade of RNA virus metagenomics is (not) enough

A decade of RNA virus metagenomics is (not) enough

Marine Oomycetes of the Genus Halophytophthora Harbor Viruses Related to Bunyaviruses

Unveiling Crucivirus Diversity by Mining Metagenomic Data

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