Genome sequence of a novel partitivirus identified from the oomycete Pythium nunn

Shiba, Kazuki; Hatta, Chiharu; Sasai, Shinsaku; Tojo, Motoaki; Ohki, Satoshi T.; Mochizuki, Tomofumi

doi:10.1007/s00705-018-3880-0

Cited by 25 publications

(20 citation statements)

References 13 publications

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“…PVaTotilike1 and 2 are rather abundant in most libraries and are most closely related to viruses recently characterized in Phythium polare and Pythium splendens ( Shiba et al. 2019 ), with conserved genomic features; therefore these two viruses are likely true P. viticola full-length mycoviruses.…”

Section: Discussionmentioning

confidence: 92%

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Analysis of the virome associated to grapevine downy mildew lesions reveals new mycovirus lineages

et al. 2020

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The obligatory biotrophic oomycetes Plasmopara viticola is the causal agent of downy mildew, a destructive disease of grapevine worldwide. So far, chemical fungicides are widely employed to limit this pathogen, but their adverse effects are stimulating the quest for environmentally friendly alternative approaches. Here we report on the search for mycoviruses that might be later developed as biocontrol agents for this pathogen. Symptomatic leaves were collected from various regions in Spain and Italy and mycelia associated to leaf lesions was harvested. Total RNA extractions were depleted of rRNA and metatranscriptomes were generated using a High-Throughput Sequencing approach. The virome associated to leaf lesions was then characterized through a bioinformatic pipeline relying on blast searches against current viral databases. Here we present an inventory of 283 new RNA viruses: 222 positive strand RNA viruses, 29 negative strand RNA viruses, 27 double stranded RNA viruses and 5 ORFan virus RdRP segments, which could not be reliably assigned to any existing group in the Riboviria. In addition to ORFan viruses, we found other surprising new evolutionary trajectories in this wide inventory of viruses. The most represented viruses in our collection are those in phylum Lenarviricota, and, among them, a group of mycovirus segments distantly related to narnaviruses, but characterized by a polymerase palm domain lacking subdomain C, with the putative GDD catalytic triad. We also provided evidence of a strict association between two RNA segments that form a new mycovirus clade of positive strand RNA in the phylum Kitrinoviricota, order Martellivirales. In the phylum Negarnaviricota, we report for the first time in the order Mononegavirales a clade of viruses that is ambisense, a feature that so far was present only in the order Bunyavirales. Furthermore, in the same phylum we detected the widespread occurrence and abundant accumulation in our libraries of a distinct mycovirus clade distantly related to the Muvirales and Goujanvirales orders, which so far include only viruses infecting invertebrates. Possible new oomycetes-specific virus clades are also described in the phylum Duplornaviricota. These data greatly expand the evolutionary history of mycoviruses adding new layers of diversity to the realm Riboviria.

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Section: Discussionmentioning

confidence: 92%

“…2018 ; Shiba et al. 2018 , 2019 ). A summary of the viruses so far studied in oomycetes was recently reviewed ( Sutela, Poimala, and Vainio 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Analysis of the virome associated to grapevine downy mildew lesions reveals new mycovirus lineages

et al. 2020

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“…Virus-like particles and/or dsRNA have been described in Pythium irregular ( Gillings et al, 1993 ). Recently, an unclassified gammapartitivirus was reported in Pythium nuun ( Shiba et al, 2018 ), a toti-like virus was also characterized from two strains of Globisporangium splendens (formerly Pythium splendes ) and three virus-like sequences, Pythium polare RNA virus 1 (PpRV1), Pythium polare RNA virus 2 (PpRV2) and PpBRV1 were detected in Pythium polare infecting mosses in the Arctic ( Sasai et al, 2018 ). In the genus Phytophthora the first virus to be reported in the USA ( Hacker et al, 2005 ) was classified as an alphaendornavirus.…”

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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“…The family accommodates five genera: Alphapartitivirus, Betapartitivirus, Cryspovirus, Deltapartitivirus, and Gammapartitivirus [59]. The genera Alphapartitivirus and Betapartitivirus are known to infect plants, ascomycetes or basidiomycetes, whereas the genus Gammapartitivirus infect ascomycetes [59] and oomycetes [60]. The genera Deltapartitivirus and Cryspovirus infect exclusively plants and protozoa, respectively [59].…”

Section: Partitiviridae and Bipartitiviridaementioning

confidence: 99%

Viruses Infecting the Plant Pathogenic Fungus Rhizoctonia solani

Abdoulaye

Foda

Kotta‐Loizou

2019

Viruses

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The cosmopolitan fungus Rhizoctonia solani has a wide host range and is the causal agent of numerous crop diseases, leading to significant economic losses. To date, no cultivars showing complete resistance to R. solani have been identified and it is imperative to develop a strategy to control the spread of the disease. Fungal viruses, or mycoviruses, are widespread in all major groups of fungi and next-generation sequencing (NGS) is currently the most efficient approach for their identification. An increasing number of novel mycoviruses are being reported, including double-stranded (ds) RNA, circular single-stranded (ss) DNA, negative sense (−)ssRNA, and positive sense (+)ssRNA viruses. The majority of mycovirus infections are cryptic with no obvious symptoms on the hosts; however, some mycoviruses may alter fungal host pathogenicity resulting in hypervirulence or hypovirulence and are therefore potential biological control agents that could be used to combat fungal diseases. R. solani harbors a range of dsRNA and ssRNA viruses, either belonging to established families, such as Endornaviridae, Tymoviridae, Partitiviridae, and Narnaviridae, or unclassified, and some of them have been associated with hypervirulence or hypovirulence. Here we discuss in depth the molecular features of known viruses infecting R. solani and their potential as biological control agents.

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Genome sequence of a novel partitivirus identified from the oomycete Pythium nunn

Cited by 25 publications

References 13 publications

Analysis of the virome associated to grapevine downy mildew lesions reveals new mycovirus lineages

Analysis of the virome associated to grapevine downy mildew lesions reveals new mycovirus lineages

Marine Oomycetes of the Genus Halophytophthora Harbor Viruses Related to Bunyaviruses

Viruses Infecting the Plant Pathogenic Fungus Rhizoctonia solani

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