•RNA-Seq datasets were used for de novo contig assembly and virus detection.•The genomes of two new mitovirus strains were described.•Occurrence of similar viruses was detected by RT-PCR in H. ...annosum and H. parviporum.
Mitoviral infections are highly common among fungi, but so far only one mitovirus has been described in Heterobasidion spp. conifer pathogens. Here, the occurrence of further mitoviruses was investigated using a previously published RNA-Seq dataset for de novo contig assembly. This allowed the identification of two additional mitovirus strains designated as Heterobasidion mitovirus 2 (HetMV2) and HetMV3 with genome lengths of ca. 2.9 and 5.0 kb. Furthermore, the occurrence of similar viruses was screened among a collection of Heterobasidion isolates using RT-PCR. Mitoviruses were detected in six more fungal isolates and two different host species, H. annosum and H. parviporum.
ABSTRACT
Soils support a myriad of organisms hosting highly diverse viromes. In this minireview, we focus on viruses hosted by true fungi and oomycetes (members of Stamenopila, Chromalveolata) ...inhabiting bulk soil, rhizosphere and litter layer, and representing different ecological guilds, including fungal saprotrophs, mycorrhizal fungi, mutualistic endophytes and pathogens. Viruses infecting fungi and oomycetes are characterized by persistent intracellular nonlytic lifestyles and transmission via spores and/or hyphal contacts. Almost all fungal and oomycete viruses have genomes composed of single-stranded or double-stranded RNA, and recent studies have revealed numerous novel viruses representing yet unclassified family-level groups. Depending on the virus–host combination, infections can be asymptomatic, beneficial or detrimental to the host. Thus, mycovirus infections may contribute to the multiplex interactions of hosts, therefore likely affecting the dynamics of fungal communities required for the functioning of soil ecosystems. However, the effects of fungal and oomycete viruses on soil ecological processes are still mostly unknown. Interestingly, new metagenomics data suggest an extensive level of horizontal virus transfer between plants, fungi and insects.
Soil-inhabiting fungi and oomycetes host diverse viruses with various effects on their hosts, potentially affecting the community structure of soil microorganisms as well as plants.
•Complete genomes of two bisegmented dsRNA viruses hosted by ectomycorrhizal fungi.•Sixty Lactarius isolates investigated originating from two boreal forest sites.•The diversity and population ...structure of both mycoviruses determined.•No interspecies virus transmission between closely related host species detected.•Both mycoviruses persisted at least 5–8 years in the forest.
Lactarius fungi belong to the Russulaceae family and have an important ecological role as ectomycorrhizal symbionts of coniferous and deciduous trees. Two Lactarius species, L. tabidus and L. rufus have been shown to harbor bisegmented dsRNA viruses belonging to an unclassified virus group including the mutualistic Curvularia thermal tolerance virus (CThTV). In this study, we characterized the first complete genome sequences of these viruses designated as Lactarius tabidus RNA virus 1 (LtRV1) and Lactarius rufus RNA virus 1 (LrRV1), both of which included two genome segments of 2241 and 2049 bp. We also analyzed spatial distribution and sequence diversity of the viruses in sixty host strains at two forest sites, and showed that the viruses are species-specific at sites where both host species co-occur. We also found that single virus isolates inhabited several different conspecific host strains, and were involved in persistent infections during up to eight years.
•High-throughput sequencing was used for virus detection in Bondarzewia berkeleyi.•The complete genome sequence of a new alphapartitivirus is characterized.•The complete genome sequence of a new ...mymona-like virus is described.•The viruses are the first ones described in species of Bondarzewia.•Genome structure and phylogenetic affiliations are discussed.
Virus communities of forest fungi remain poorly characterized. In this study, we detected two new viruses co-infecting an isolate of the polypore fungus Bondarzewia berkeleyi using high-throughput sequencing. One of them was a putative new partitivirus designated as Bondarzewia berkeleyi partitivirus 1 (BbPV1), with two linear dsRNA genome segments of 1928 and 1863 bp encoding a putative RNA-dependent RNA polymerase (RdRP) of 591 aa and a putative capsid protein of 538 aa. The other virus, designated as Bondarzewia berkeleyi negative-strand RNA virus 1 (BbNSRV1), had a non-segmented negative-sense RNA genome of 10,983 nt and was related to members of family Mymonaviridae. The BbNSRV1 genome includes six predicted open reading frames (ORFs) of 279, 425, 230, 174, 200 and 1970 aa. The longest ORF contained conserved regions corresponding to Mononegavirales RdRP and mRNA-capping enzyme region V constituting the mononegavirus Large protein. In addition, a low level of sequence identity was detected between the putative nucleocapsid protein-coding ORF2 of Lentinula edodes negative-strand RNA virus 1 and BbNSRV1. The viruses characterized in this study are the first ones described in Bondarzewia spp., and BbNSRV1 is the second mymona-like virus described in a basidiomycete host.
This report describes the complete genome sequence of a double-stranded RNA (dsRNA) virus infecting the oomycetous plant pathogen
Phytophthora cactorum
. The virus genome consists of a single dsRNA ...segment of 5699 bp with two open reading frames predicted to overlap with each other and encoding a putative capsid protein of 705 aa and an RNA-dependent RNA polymerase of 779 aa. Sequence comparisons indicated that this virus, designated as “Phytophthora cactorum RNA virus 1” (PcRV1), shares the highest sequence similarity with the unclassified Pythium splendens RNA virus 1 (58% RdRp aa sequence identity). Phylogenetic analysis revealed that these two oomycete viruses group together with Giardia lamblia virus (GVL; family
Totiviridae
) and several unclassified toti-like viruses from arthropods, fish and fungi. This is the first report of a toti-like virus in a member of the genus
Phytophthora
and the first virus characterized in
P. cactorum.
•Family Partitiviridae has undergone a taxonomic reorganization.•Four new genera of fungal or plant partitiviruses have been added to the family.•The three former genera of fungal or plant ...partitiviruses have been eliminated.•Other recent progress of note in partitivirus research is summarized.•Partitivirus effects on their hosts appear not to be cryptic in many cases.
Phylogenetic analyses have prompted a taxonomic reorganization of family Partitiviridae (encapsidated, bisegmented dsRNA viruses that infect plants, fungi, or protozoa), the focus of this review. After a brief introduction to partitiviruses, the taxonomic changes are discussed, including replacement of former genera Partitivirus, Alphacryptovirus, and Betacryptovirus, with new genera Alphapartitivirus, Betapartitivirus, Gammapartitivirus, and Deltapartitivirus, as well as redistribution of species among these new genera. To round out the review, other recent progress of note in partitivirus research is summarized, including discoveries of novel partitivirus sequences by metagenomic approaches and mining of sequence databases, determinations of fungal partitivirus particle structures, demonstrations of fungal partitivirus transmission to new fungal host species, evidence for other aspects of partitivirus–host interactions and host effects, and identification of other fungal or plant viruses with some similarities to partitiviruses. Some outstanding questions are also discussed.
Summary
Eighty‐eight Phytophthora cactorum strains isolated from crown or leather rot of strawberry in 1971–2019 were screened for viruses using RNA‐seq and RT‐PCR. Remarkably, all but one isolate ...were virus‐infected, most of them harbouring more than one virus of different genera or species. The most common virus occurring in 94% of the isolates was the Phytophthora cactorum RNA virus 1 (PcRV1) resembling members of Totiviridae. Novel viruses related to members of Endornaviridae, named Phytophthora cactorum alphaendornaviruses 1‐3 (PcAEV1‐3), were found in 57% of the isolates. Four isolates hosted viruses with affinities to Bunyaviridae, named Phytophthora cactorum bunyaviruses 1‐3 (PcBV1‐3), and a virus resembling members of the proposed genus ‘Ustivirus’, named Phytophthora cactorum usti‐like virus (PcUV1), was found in a single isolate. Most of the virus species were represented by several distinct strains sharing ≥81.4% aa sequence identity. We found no evidence of spatial differentiation but some temporal changes in the P. cactorum virus community were observed. Some isolates harboured two or more closely related strains of the same virus (PcAEV1 or PcRV1) sharing 86.6%–96.4% nt identity in their polymerase sequence. This was surprising as viruses with such a high similarity are typically mutually exclusive.
species are highly destructive basidiomycetous conifer pathogens of the Boreal forest region. Earlier studies have revealed dsRNA virus infections of families
and
in
strains, and small RNA deep ...sequencing has also identified infections of
members in these fungi. In this study, the virome of
was examined for the first time by RNA-Seq using total RNA depleted of rRNA. This method successfully revealed new viruses representing two established (+)ssRNA virus families not found earlier in
:
and
. In addition, we identified the presence of a recently described virus group tentatively named "ambiviruses" in
. The
isolates included in the study originated from experimental forest sites located within 0.7 km range from each other, and a population analysis including 43 isolates was conducted at one of the experimental plots to establish the prevalence of the newly identified viruses in clonally spreading
individuals. Our results indicate that viral infections are considerably more diverse and common among
isolates than known earlier and include ssRNA viruses with high prevalence and interspecies variation.
Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has ...undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios.
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