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

Abstract

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.

Interannual dynamics, diversity and evolution of the virome in Sclerotinia sclerotiorum from a single crop field

“…Sclerotinia sclerotiorum ophiovirus-like virus 1 (SsOpLV1) with 7,817 nt in length shows the highest similarity to Fusarium poae negative-stranded virus 1 within the recently proposed Mycoaspiviridae family ( Chiapello et al 2020 ). SsOpLV1 contained two linearly arranged nonoverlapping ORFs ( Supplementary Fig.…”

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

“…This may indicate that the co-infection of these unrelated viral genera is stable enough and they do not exclude each other. Indeed, multiple viral infections are known to occur in fungi and oomycetes in nature [ 16 , 17 , 20 , 46 , 47 , 48 , 49 , 50 , 51 , 52 ]. However, the virus-virus interactions and the limits of accumulation of multiple viruses in a single host remain unclear [ 53 ].…”

“…Furthermore, two novel endornaviruses were found co-infecting isolates of an unidentified Phytophthora species causing asparagus rot in Japan [ 12 ]. In other oomycetes, several (+)ssRNA viruses have been described in obligate biotrophic downy mildews including Plasmopara halstedii and Plasmopara viticola [ 13 , 14 , 15 , 16 , 17 ]. Virus-like particles and/or dsRNA have been observed in Pythium irregular [ 18 ], an unclassified gammapartitivirus was reported in Pythium nuun [ 19 ], a toti-like virus was also described 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 Pythium polare bunya-like RNA virus 1 (PpBRV1) were identified in Pythium polare infecting mosses in the Arctic [ 20 ].…”

Characterization of a Novel Mitovirus of the Sand Fly Lutzomyia longipalpis Using Genomic and Virus–Host Interaction Signatures

“…In addition, it has been proposed that these genera might have been evolved from Leviviridae -ancestors that infected bacterial endosymbionts, some of which may have generated mitochondria [ 39 , 45 , 75 ]. A phylogenetic reconstruction using RdRp sequences ( Figure 2 ) revealed that Lul-MV-1 is closely related to the Plasmopara viticola lesion-associated mitovirus 56 (QIR30279), a fungal mitovirus found in grapevine [ 76 ], and to a slightly lesser extent to the Wenling narna-like virus 9 (YP_009337200), identified in crustaceans [ 15 ]. The narnaviruses constituted a sister clade composed of viruses infecting either fungal or insect hosts.…”