Complete genome sequence of a novel toti-like virus from the plant-pathogenic oomycete Phytophthora cactorum

Poimala, Anna; Vainio, Eeva J.

doi:10.1007/s00705-020-04642-2

Cited by 17 publications

(28 citation statements)

References 13 publications

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“…Alternative initiation (non-AUG codons) has been reported in many plant viruses but also in fungi and oomycetes. Phytophthora cactorum RNA virus 1 (PcRV1), Pythium polare RNA virus 1 (PpRV1), Ophiostoma minus totivirus (OmV) start RdRp-ORF with Leucine codons [ 11 , 20 , 46 ]. Non-canonical elongation (ribosomal frameshifting) is typical in fungal viruses of the families Hypoviridae , Megabinaviridae , Fusagraviridae and Totiviridae .…”

Section: Resultsmentioning

confidence: 99%

“…PiRV2, which is 100% transmittable through asexual spores, has been demonstrated to enhance the sporangia production of P. infestans , thereby boosting the virulence of its host [ 10 ]. Phytophthora cactorum RNA virus 1 (PcRV1), a toti-like virus, was recently reported in an isolate of the pathogen Phytophthora cactorum from silver birch [ 11 ]. Furthermore, two novel endornaviruses were found co-infecting isolates of an unidentified Phytophthora species causing asparagus rot in Japan [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

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Multiple Viral Infections Detected in Phytophthora condilina by Total and Small RNA Sequencing

Botella

Jung

2021

Viruses

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Marine oomycetes have recently been shown to be concurrently infected by (−)ssRNA viruses of the order Bunyavirales. In this work, even higher virus variability was found in a single isolate of Phytophthora condilina, a recently described member of Phytophthora phylogenetic Clade 6a, which was isolated from brackish estuarine waters in southern Portugal. Using total and small RNA-seq the full RdRp of 13 different potential novel bunya-like viruses and two complete toti-like viruses were detected. All these viruses were successfully confirmed by reverse transcription polymerase chain reaction (RT-PCR) using total RNA as template, but complementarily one of the toti-like and five of the bunya-like viruses were confirmed when dsRNA was purified for RT-PCR. In our study, total RNA-seq was by far more efficient for de novo assembling of the virus sequencing but small RNA-seq showed higher read numbers for most viruses. Two main populations of small RNAs (21 nts and 25 nts-long) were identified, which were in accordance with other Phytophthora species. To the best of our knowledge, this is the first study using small RNA sequencing to identify viruses in Phytophthora spp.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Multiple Viral Infections Detected in Phytophthora condilina by Total and Small RNA Sequencing

Botella

Jung

2021

Viruses

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“…complex ( A. alternata and A. arborescens ). Occurrence of such fungi as endophytes (and here probably also as microorganisms of the phyllosphere) in grapevine is common and was previously studied ( Polizzotto et al. 2012 ; Tao et al.…”

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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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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“…Recently, PiRV2, known to be 100% transmittable through asexual spores, was shown to stimulate sporangia production and enhance the virulence of P. infestans (Cai et al, 2019). Phytophthora cactorum RNA virus 1 (PcRV1), a toti-like virus, has been newly described in an isolate of Phytophthora cactorum collected from a trunk lesion on silver birch in Denmark (Poimala and Vainio, 2020).…”

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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Complete genome sequence of a novel toti-like virus from the plant-pathogenic oomycete Phytophthora cactorum

Cited by 17 publications

References 13 publications

Multiple Viral Infections Detected in Phytophthora condilina by Total and Small RNA Sequencing

Multiple Viral Infections Detected in Phytophthora condilina by Total and Small RNA Sequencing

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

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