Molecular characterization of two evolutionarily distinct endornaviruses co-infecting common bean (Phaseolus vulgaris)

Bell pepper endornavirus alters green peach aphid (Hemiptera: Aphididae) host choice and population dynamics

Bell pepper endornavirus (BPEV) Alphaendornavirus capsici (Endornaviridae) is an RNA virus that infects many pepper (Capsicum annuum) horticultural types and is seed transmitted. BPEV does not cause apparent symptoms and is found at every plant developmental stage. During the domestication of bell pepper, plant breeders, unaware of the existence of endornaviruses in the germplasm, selected endornavirus-infected genotypes. This could be an indication that the presence of endornaviruses in this crop is beneficial. Among the possible beneficial effects that endornaviruses may provide to their host could include tolerance or resistance to biotic and abiotic agents and, therefore, may have evolved a symbiotic relationship with their hosts. With this in mind, we set out to determine host preference, host suitability, and population dynamics of green peach aphid Myzus persicae (Sulzer) on BPEV-infected and virus-free bell pepper near-isogenic lines. During choice bioassay experiments, we observed that a higher proportion of M. persicae adults settled on BPEV noninfected leaves as compared to BPEV-infected leaves. Life table analysis revealed that M. persicae performed less well on BPEV-infected leaf tissues, with reductions in longevity, progeny, and intrinsic rate of increase. These results indicate BPEV is beneficial to its host, protecting against an important generalist pest.

Mycoviruses from Aspergillus fungi involved in fermentation of dried bonito

Fungi are exploited for fermentation of foods such as cheese, Japanese sake, and soy sauce. However, the diversity of viruses that infect fungi involved in food fermentation is poorly understood. Fermented dried bonito ("katsuobushi") is one of the most important processed marine products in Japan. Fungi involved in katsuobushi fermentation are called katsuobushi molds, and Aspergillus spp. have been reported to be dominant on the surface of katsuobushi during fermentation. Because various mycoviruses have been found in members of the genus Aspergillus, we hypothesized that katsuobushi molds are also infected with mycoviruses. Here, we describe seven novel mycoviruses belonging to six families (Chrysoviridae, Fusariviridae, Mitoviridae, Partitiviridae, Polymycoviridae, and Pseudototiviridae) from isolated katsuobushi molds (Aspergillus chevalieri and A. sulphureus) detected by fragmented and primer-ligated double-stranded RNA sequencing. Aspergillus chevalieri fusarivirus 1 has a unique bi-segmented genome, whereas other known fusariviruses have a single genomic segment. Phenotypic comparison between the parental A. chevalieri strain infected with Aspergillus chevalieri polymycovirus 1 (AchPmV1) and isogenic AchPmV1-free isolates indicated that AchPmV1 inhibits the early growth of the host. This study reveals the diversity of mycoviruses that infect katsuobushi molds, and provides insight into the effect of mycoviruses on fungi involved in fermentation.

Complete genome sequence of lima bean endornavirus 1: a putative new member of the genus Alphaendornavirus (family Endornaviridae)

In this study, we completely sequenced the genome of a new member of the genus Alphaendornavirus, family Endornaviridae, from lima bean (Phaseolus lunatus), for which we propose the name "lima bean endornavirus 1" (LbEV1). The complete genome of LbEV1 consists of 15,265 nucleotides, including a stretch of 12 cytosine residues at its 3' end, and contains a long single open reading frame (ORF) coding for a 4980-aa-long polyprotein. Analysis of the polyprotein sequence revealed the presence of four conserved functional domains (in order from the N- to C-terminus): viral helicase 1, peptidase _C97, glycosyltransferase_GTB-type, and viral RNA-dependent RNA polymerase (RdRP). The LbEV1 polyprotein showed the highest amino acid sequence similarity (63% identity and 98% coverage) to Phaseolus vulgaris endornavirus 3 (PvEV3) and also showed 42% identity (95% coverage) to Geranium carolinianum endornavirus. Phylogenetic analysis based on the viral RdRp domain showed that LbEV1 belongs to a subclade within the genus Alphaendornavirus that includes three other viruses infecting plants of the genus Phaseolus.

Characterization of a novel endornavirus isolated from the phytopathogenic fungus Rhizoctonia solani

Rhizoctonia solani endornavirus 8 (RsEV8) was isolated from strain XY175 of Rhizoctonia solani AG-1 IA. The full-length genome of RsEV8 is 16,147 nucleotides (nt) in length and contains a single open reading frame that encodes a large polyprotein of 5227 amino acids. The polyprotein contains four conserved domains: viral methyltransferase, putative DEAH box helicase, viral helicase, and RNA-dependent RNA polymerase (RdRp). RsEV8 has a shorter 3'-UTR (58 nt) and a longer 5'-UTR (404 nt). A multiple sequence alignment indicated that the RdRp of RsEV8 possesses eight typical RdRp motifs. According to a BLASTp analysis, RsEV8 shares 39.31% sequence identity with Rhizoctonia cerealis endornavirus-1084-7. Phylogenetic analysis demonstrated that RsEV8 clusters with members of the genus Betaendornavirus.

Mycoviruses: Antagonistic Potential, Fungal Pathogenesis, and Their Interaction with Rhizoctonia solani

Mycoviruses, or fungal viruses, are prevalent in all significant fungal kingdoms and genera. These low-virulence viruses can be used as biocontrol agents to manage fungal diseases. These viruses are divided into 19 officially recognized families and 1 unclassified genus. Mycoviruses alter sexual reproduction, pigmentation, and development. Spores and fungal hypha spread mycoviruses. Isometric particles mostly encapsulate dsRNA mycoviruses. The widespread plant-pathogenic fungus Rhizoctonia solani, which has caused a rice sheath blight, has hosted many viruses with different morphologies. It causes significant crop diseases that adversely affect agriculture and the economy. Rice sheath blight threatens the 40% of the global population that relies on rice for food and nutrition. This article reviews mycovirology research on Rhizoctonia solani to demonstrate scientific advances. Mycoviruses control rice sheath blight. Hypovirulence-associated mycoviruses are needed to control R. solani since no cultivars are resistant. Mycoviruses are usually cryptic, but they can benefit the host fungus. Phytopathologists may use hypovirulent viruses as biological control agents. New tools are being developed based on host genome studies to overcome the intellectual challenge of comprehending the interactions between viruses and fungi and the practical challenge of influencing these interactions to develop biocontrol agents against significant plant pathogens.

Identification and characterization of Phaseolus vulgaris endornavirus 1, 2 and 3 in common bean cultivars of East Africa

Persistent viruses include members of the family Endornavirus that cause no apparent disease and are transmitted exclusively via seed or pollen. It is speculated that these RNA viruses may be mutualists that enhance plant resilience to biotic and abiotic stresses. Using reverse transcription coupled polymerase chain reactions, we investigated if common bean (Phaseolus vulgaris L.) varieties popular in east Africa were hosts for Phaseolus vulgaris endornavirus (PvEV) 1, 2 or 3. Out of 26 bean varieties examined, four were infected with PvEV1, three were infected with both PvEV1 and PvEV2 and three had infections of all three (PvEV) 1, 2 and 3. Notably, this was the first identification of PvEV3 in common bean from Africa. Using high-throughput sequencing of two east African bean varieties (KK022 and KK072), we confirmed the presence of these viruses and generated their genomes. Intra- and inter-species sequence comparisons of these genomes with comparator sequences from GenBank revealed clear species demarcation. In addition, phylogenetic analyses based on sequences generated from the helicase domains showed that geographical distribution does not correlate to genetic relatedness or the occurrence of endornaviruses. These findings are an important first step towards future investigations to determine if these viruses engender positive effects in common bean, a vital crop in east Africa.

Investigating the interactions of endornaviruses with each other and with other viruses in common bean, Phaseolus vulgaris

BACKGROUND

Plant viruses of the genus Alphaendornavirus are transmitted solely via seed and pollen and generally cause no apparent disease. It has been conjectured that certain plant endornaviruses may confer advantages on their hosts through improved performance (e.g., seed yield) or resilience to abiotic or biotic insult. We recently characterised nine common bean (Phaseolus vulgaris L.) varieties that harboured either Phaseolus vulgaris endornavirus (PvEV1) alone, or PvEV1 in combination with PvEV2 or PvEV1 in combination with PvEV2 and PvEV3. Here, we investigated the interactions of these endornaviruses with each other, and with three infectious pathogenic viruses: cucumber mosaic virus (CMV), bean common mosaic virus (BCMV), and bean common mosaic necrosis virus (BCMNV).

RESULTS

In lines harbouring PvEV1, PvEV1 and PvEV2, or PvEV1, PvEV2 plus PvEV3, the levels of PvEV1 and PvEV3 RNA were very similar between lines, although there were variations in PvEV2 RNA accumulation. In plants inoculated with infectious viruses, CMV, BCMV and BCMNV levels varied between lines, but this was most likely due to host genotype differences rather than to the presence or absence of endornaviruses. We tested the effects of endornaviruses on seed production and seedborne transmission of infectious pathogenic viruses but found no consistent relationship between the presence of endornaviruses and seed yield or protection from seedborne transmission of infectious pathogenic viruses.

CONCLUSIONS

It was concluded that endornaviruses do not interfere with each other's accumulation. There appears to be no direct synergy or competition between infectious pathogenic viruses and endornaviruses, however, the effects of host genotype may obscure interactions between endornaviruses and infectious viruses. There is no consistent effect of endornaviruses on seed yield or susceptibility to seedborne transmission of other viruses.

Successful full-length genomic cloning and characterization of site-specific nick structures of Phytophthora endornaviruses 2 and 3 in yeast, Saccharomyces cerevisiae

Two endornaviruses, Phytophthora endornavirus 2 (PEV2) and Phytophthora endornavirus 3 (PEV3), have been discovered in pathogens targeting asparagus. In this study, we analyzed the nick structure in the RNA genomes of PEV2 and PEV3 in the host oomycetes. Northern blot hybridization using positive and negative strand-specific RNA probes targeting the 5' and 3' regions of PEV2 and PEV3 RNA genomes revealed approximately 1.0 kilobase (kb) RNA fragments located in the 5' regions of the two genomes. 3' RACE analysis determined that the size of the RNA fragments were 958 nucleotides (nt) for PEV2 and 968 nt for PEV3. We have successfully constructed full-length cDNA clones of the entire RNA genomes of PEV2 and PEV3 using a homologous recombination system in the yeast, Saccharomyces cerevisiae. These full-length cDNA sequences were ligated downstream of a constitutive expression promoter (TDH3) or a galactose-inducing promoter (GAL1) in the shuttle vector to enable the production of the full-length RNA transcripts of PEV2 and PEV3 in yeast cells. Interestingly, a 1.0 kb RNA fragment from the PEV3 positive-strand transcript was also detected with a 5'-region RNA probe, indicating that site-specific cleavage also occurred in yeast cells. Further, when PEV2 or PEV3 mRNA was overexpressed under the GAL1 promoter, yeast cell growth was suppressed. A fusion protein combining EGFP to the N-terminus of the full-length PEV2 ORF or C-terminus of the full-length PEV3 ORF was expressed, and allowed PEV2 and PEV3 ORFs to be successfully visualized in yeast cells. Expression of the fusion protein also revealed presence of heterogeneous bodies in the cells.

Composition of the alfalfa pathobiome in commercial fields

Through the recent advances of modern high-throughput sequencing technologies, the "one microbe, one disease" dogma is being gradually replaced with the principle of the "pathobiome". Pathobiome is a comprehensive biotic environment that not only includes a diverse community of all disease-causing organisms within the plant but also defines their mutual interactions and resultant effect on plant health. To date, the concept of pathobiome as a major component in plant health and sustainable production of alfalfa (Medicago sativa L.), the most extensively cultivated forage legume in the world, is non-existent. Here, we approached this subject by characterizing the biodiversity of the alfalfa pathobiome using high-throughput sequencing technology. Our metagenomic study revealed a remarkable abundance of different pathogenic communities associated with alfalfa in the natural ecosystem. Profiling the alfalfa pathobiome is a starting point to assess known and identify new and emerging stress challenges in the context of plant disease management. In addition, it allows us to address the complexity of microbial interactions within the plant host and their impact on the development and evolution of pathogenesis.

Snake River alfalfa virus, a persistent virus infecting alfalfa (Medicago sativa L.) in Washington State, USA

Here we report an occurrence of Snake River alfalfa virus (SRAV) in Washington state, USA. SRAV was recently identified in alfalfa (Medicago sativa L.) plants and western flower thrips in south-central Idaho and proposed to be a first flavi-like virus identified in a plant host. We argue that the SRAV, based on its prevalence in alfalfa plants, readily detectable dsRNA, genome structure, presence in alfalfa seeds, and seed-mediated transmission is a persistent new virus distantly resembling members of the family Endornaviridae.

Genetic diversity and phylogenetic characteristics of viruses in lily plants in Beijing

Lily (Lilium) is an important bulbous perennial herb that is frequently infected by one or more viruses. To investigate the diversity of lily viruses, lilies with virus-like symptoms in Beijing were collected to perform small RNA deep sequencing. Then, the 12 complete and six nearly full-length viral genomes, including six known viruses and two novel viruses were determined. Based on sequence and phylogenetic analyses, two novel viruses were considered to be members of the genera Alphaendornavirus (Endornaviridae) and Polerovirus (Solemoviridae). These two novel viruses were provisionally named lily-associated alphaendornavirus 1 (LaEV-1) and lily-associated polerovirus 1 (LaPV-1). Based on sequence, phylogenetic and recombination analyses, strawberry latent ringspot virus (SLRSV) in the genus Stralarivirus (Secoviridae) was identified for the first time in China, and shown to exhibit the highest nucleotide (nt) diversity among the available full-length SLRSV genome sequences, with the highest identities of 79.5% for RNA1 and 80.9% for RNA2. Interestingly, the protease cofactor region in RNA1 was 752 aa in length, whereas those of the other 27 characterized isolates ranged from 700-719 aa in length. The genome sequences of lily virus A (Potyvirus), lily virus X (Potexvirus), and plantago asiatica mosaic virus (Potexvirus) exhibited varying degrees of sequence diversity at the nucleotide level compared with their corresponding characterized isolates. In addition, plantago asiatica mosaic virus (PlAMV) tended to cluster on a host species-basis. One identified lily mottle virus (Potyvirus) isolate was detected as a recombinant, and which clustered in a different group with four other isolates. Seven identified lily symptomless virus (Carlavirus) isolates, including one recombinant, were clustered into three clades. Our results revealed the genetic diversity of lily-infecting viruses, and sequence insertion, host species and recombination are factors that likely contribute to this diversity. Collectively, our results provide useful information regarding the control of viral disease in lily.

Molecular characterization of a novel endornavirus isolated from Ophiostoma bicolor associated with bark beetles

Ophiostoma bicolor is a pathogenic fungus associated with bark beetles that can cause serious damage to host plants. In this study, a novel fungal virus, "Ophiostoma bicolor endornavirus 1" (ObEV1), was obtained from O. bicolor, and its complete genome sequence was determined. ObEV1 has a single-stranded positive-sense (+ ss) RNA genome of 10,119 nucleotides. Sequence annotation and comparison showed that the viral genome has a single large open reading frame (ORF) encoding a polyprotein of 362.48 kDa. The polyprotein contains seven conserved domains: RNA-dependent RNA polymerase (RdRp), viral RNA helicase 1 (VHel1), viral methyltransferase (VMet), DEAD-like helicase (DEXDc), gliding-GltJ (G1), large tegument protein UL36 (PHA), and YlqF-related-GTPase (Y). Sequence comparisons and phylogenetic analysis showed that ObEV1 is a novel mycovirus belonging to the genus Betaendornavirus of the family Endornaviridae. This is the first report of a mycovirus in the ophiostomatoid fungus O. bicolor.

Diverse RNA Viruses Associated with Diatom, Eustigmatophyte, Dinoflagellate, and Rhodophyte Microalgae Cultures

Unicellular microalgae are of immense ecological importance with growing commercial potential in industries such as renewable energy, food, and pharmacology. Viral infections can have a profound impact on the growth and evolution of their hosts. However, very little is known of the diversity within, and the effect of, unicellular microalgal RNA viruses. In addition, identifying RNA viruses in these organisms that could have originated more than a billion years ago constitutes a robust data set to dissect molecular events and address fundamental questions in virus evolution. We assessed the diversity of RNA viruses in eight microalgal cultures, including representatives from the diatom, eustigmatophyte, dinoflagellate, red algae, and euglenid groups. Using metatranscriptomic sequencing combined with bioinformatic approaches optimized to detect highly divergent RNA viruses, we identified 10 RNA virus sequences, with nine constituting new viral species. Most of the newly identified RNA viruses belonged to the double-stranded Totiviridae, Endornaviridae, and Partitiviridae, greatly expanding the reported host range for these families. Two new species belonging to the single-stranded RNA viral clade Marnaviridae, commonly associated with microalgal hosts, were also identified. This study highlights that a substantial diversity of RNA viruses likely exists undetected within the unicellular microalgae. It also highlights the necessity for RNA viral characterization and for investigation of the effects of viral infections on microalgal physiology, biology, and growth, considering their environmental and industrial roles. IMPORTANCE Our knowledge of the diversity of RNA viruses infecting microbial algae-the microalgae-is minimal. However, describing the RNA viruses infecting these organisms is of primary importance at both the ecological and economic scales because of the fundamental roles these organisms play in aquatic environments and their growing value across a range of industrial fields. Using metatranscriptomic sequencing, we aimed to reveal the RNA viruses present in cultures of eight microalgae species belonging to the diatom, dinoflagellate, eustigmatophyte, rhodophyte, and euglena major clades of algae. Accordingly, we identified 10 new divergent RNA virus species belonging to RNA virus families as diverse as the double-stranded Totiviridae, Endornaviridae, and Partitiviridae and the single-stranded Marnaviridae. By expanding the known diversity of RNA viruses infecting unicellular eukaryotes, this study contributes to a better understanding of the early evolution of the virosphere and will inform the use of microalgae in industrial applications.

Identification of a novel alphaendornavirus from Lonicera maackii

A new alphaendornavirus, tentatively named "Lonicera maackii alphaendornavirus" (LmEV), was identified in a Lonicera maackii plant in Beijing, China, with leaf abnormality of interveinal chlorosis, and its complete genome sequence was determined using small-RNA deep sequencing. The RNA genome of LmEV is 16,176 nt in length and contains a large open reading frame encoding a polyprotein of 5363 aa with conserved domains including a cysteine-rich region, a viral helicase, and an RNA-dependent RNA polymerase. Sequence comparisons showed that LmEV shared the highest nt and aa sequence identity with Vicia faba alphaendornavirus (VfEV) of the genus Alphaendornavirus. In phylogenetic analysis of the RdRp aa sequence LmEV clustered with members of the genus Alphaendornavirus, closest to VfEV. To our knowledge, this is the first report of a novel alphaendornavirus identified in Lonicera maackii. Its effect on the host plant, if any, remains to be investigated.

Complete nucleotide sequence of an alphaendornavirus isolated from common buckwheat (Fagopyrum esculentum)

A double-stranded RNA (dsRNA) of approximately 16 kbp was isolated from symptomless common buckwheat (Fagopyrum esculentum) plants. The size of the dsRNA suggested that it was the replicative form of an endornavirus. The dsRNA was sequenced, and it consisted of 15,677 nt, containing a single open reading frame that potentially encoded a polyprotein of 5190 aa. The polyprotein contained conserved domains for a viral methyltransferase, viral RNA helicase 1, MSCRAMM family adhesion SdrC, UDP-glycosyltransferase, and viral RNA-dependent RNA polymerase 2. A site-specific nick in the plus strand was detected near the 5' end of the dsRNA. BLASTp analysis showed that the polyprotein shared the highest identity with the polyprotein of winged bean endornavirus 1. Results of phylogenetic analysis supported placing this novel virus from common buckwheat, which was provisionally named "Fagopyrum esculentum endornavirus 1", in the genus Alphaendornavirus of the family Endornaviridae.

Diversity and Distribution of Viruses Infecting Wild and Domesticated Phaseolus spp. in the Mesoamerican Center of Domestication

Viruses are an important disease source for beans. In order to evaluate the impact of virus disease on Phaseolus biodiversity, we determined the identity and distribution of viruses infecting wild and domesticated Phaseolus spp. in the Mesoamerican Center of Domestication (MCD) and the western state of Nayarit, Mexico. We used small RNA sequencing and assembly to identify complete or near-complete sequences of forty-seven genomes belonging to nine viral species of five genera, as well as partial sequences of two putative new endornaviruses and five badnavirus- and pararetrovirus-like sequences. The prevalence of viruses in domesticated beans was significantly higher than in wild beans (97% vs. 19%; p < 0.001), and all samples from domesticated beans were positive for at least one virus species. In contrast, no viruses were detected in 80-83% of the samples from wild beans. The Bean common mosaic virus and Bean common mosaic necrosis virus were the most prevalent viruses in wild and domesticated beans. Nevertheless, Cowpea mild mottle virus, transmitted by the whitefly Bemisia tabaci, has the potential to emerge as an important pathogen because it is both seed-borne and a non-persistently transmitted virus. Our results provide insights into the distribution of viruses in cultivated and wild Phaseolus spp. and will be useful for the identification of emerging viruses and the development of strategies for bean viral disease management in a center of diversity.

Genome structure and diversity of novel endornaviruses from wheat sharp eyespot pathogen Rhizoctonia cerealis

Rhizoctonia cerealis (teleomorph Ceratobasidium cereale) is a soil-borne plant pathogenic fungus that can cause sharp eyespot in wheat or yellow patch in grasses. In this study, 21 new endornavirus genomes were obtained from five R. cerealis strains through the high-throughput sequencing of viral double-stranded RNA. Eighteen viruses were identified as Alphaendornavirus, and three viruses were identified as new species of Betaendornavirus on the basis of the phylogenetic analysis of the deduced amino acid sequences of RNA-dependent RNA polymerase. Notably, 12 of the new alphaendornaviruses could encode two open reading frames (ORFs), which were a rare feature of Endornaviridae. The amino acid sequences encoded by ORF2 from different endornaviruses had very low identity, and their functions and evolution origins remained unclear. Different endornavirus species with remarkably different genome structures could be found in the same R. cerealis strain. This study indicated that endornaviruses are common in R. cerealis and display wide diversity. Betaendornaviruses were found in R. cerealis, and a new species was proposed. This study is the first to report that the endornaviruses from R. cerealis can encode two ORFs and enhances our understanding of the viruses in the Endornaviridae family.

Two Novel Endornaviruses Co-infecting a Phytophthora Pathogen of Asparagus officinalis Modulate the Developmental Stages and Fungicide Sensitivities of the Host Oomycete

Two novel endornaviruses, Phytophthora endornavirus 2 (PEV2) and Phytophthora endornavirus 3 (PEV3) were found in isolates of a Phytophthora pathogen of asparagus collected in Japan. A molecular phylogenetic analysis indicated that PEV2 and PEV3 belong to the genus Alphaendornavirus. The PEV2 and PEV3 genomes consist of 14,345 and 13,810 bp, and they contain single open reading frames of 4,640 and 4,603 codons, respectively. Their polyproteins contain the conserved domains of an RNA helicase, a UDP-glycosyltransferase, and an RNA-dependent RNA polymerase, which are conserved in other alphaendornaviruses. PEV2 is closely related to Brown algae endornavirus 2, whereas PEV3 is closely related to Phytophthora endornavirus 1 (PEV1), which infects a Phytophthora sp. specific to Douglas fir. PEV2 and PEV3 were detected at high titers in two original Phytophthora sp. isolates, and we found a sub-isolate with low titers of the viruses during subculture. We used the high- and low-titer isolates to evaluate the effects of the viruses on the growth, development, and fungicide sensitivities of the Phytophthora sp. host. The high-titer isolates produced smaller mycelial colonies and much higher numbers of zoosporangia than the low-titer isolate. These results suggest that PEV2 and PEV3 inhibited hyphal growth and stimulated zoosporangium formation. The high-titer isolates were more sensitive than the low-titer isolate to the fungicides benthiavalicarb-isopropyl, famoxadone, and chlorothalonil. In contrast, the high-titer isolates displayed lower sensitivity to the fungicide metalaxyl (an inhibitor of RNA polymerase I) when compared with the low-titer isolate. These results indicate that persistent infection with PEV2 and PEV3 may potentially affect the fungicide sensitivities of the host oomycete.

Phenotypic and Molecular Biological Analysis of Polymycovirus AfuPmV-1M From Aspergillus fumigatus: Reduced Fungal Virulence in a Mouse Infection Model

The filamentous fungal pathogen Aspergillus fumigatus is one of the most common causal agents of invasive fungal infection in humans; the infection is associated with an alarmingly high mortality rate. In this study, we investigated whether a mycovirus, named AfuPmV-1M, can reduce the virulence of A. fumigatus in a mouse infection model. AfuPmV-1M has high sequence similarity to AfuPmV-1, one of the polymycovirus that is a capsidless four-segment double-stranded RNA (dsRNA) virus, previously isolated from the genome reference strain of A. fumigatus, Af293. However, we found the isolate had an additional fifth dsRNA segment, referred to as open reading frame 5 (ORF5), which has not been reported in AfuPmV-1. We then established isogenic lines of virus-infected and virus-free A. fumigatus strains. Mycovirus infection had apparent influences on fungal phenotypes, with the virus-infected strain producing a reduced mycelial mass and reduced conidial number in comparison with these features of the virus-free strain. Also, resting conidia of the infected strain showed reduced adherence to pulmonary epithelial cells and reduced tolerance to macrophage phagocytosis. In an immunosuppressed mouse infection model, the virus-infected strain showed reduced mortality in comparison with mortality due to the virus-free strain. RNA sequencing and high-performance liquid chromatography (HPLC) analysis showed that the virus suppressed the expression of genes for gliotoxin synthesis and its production at the mycelial stage. Conversely, the virus enhanced gene expression and biosynthesis of fumagillin. Viral RNA expression was enhanced during conidial maturation, conidial germination, and the mycelial stage. We presume that the RNA or translation products of the virus affected fungal phenotypes, including spore formation and toxin synthesis. To identify the mycovirus genes responsible for attenuation of fungal virulence, each viral ORF was ectopically expressed in the virus-free KU strain. We found that the expression of ORF2 and ORF5 reduced fungal virulence in the mouse model. In addition, ORF3 affected the stress tolerance of host A. fumigatus in culture. We hypothesize that the respective viral genes work cooperatively to suppress the pathogenicity of the fungal host.

Identification of a novel endornavirus in Geranium carolinianum and occurrence within three agroecosystems

A putative endornavirus was detected in Carolina geranium (Geranium carolinianum) in Louisiana, USA. The virus was provisionally named Geranium carolinianum endornavirus 1 (GcEV1). The viral RNA was sequenced, and it consisted of 14,625 nt containing a single ORF coding a putative polyprotein of 4815 aa with conserved domains for a helicase 1, peptidase C97, glycosyl transferase GTB-type, and RNA-dependent RNA polymerase 2. The 5'end consisted of 130 nt while the 3'end consisted of 54 nt ending in nine cytosine residues. The closest relative to GcEV1 was Phaseolus vulgaris endornavirus 3. In phylogenetic analyses, GcEV1 clustered with members of the genus Alphaendornavirus. GcEV1 was detected in 57 of 60 G. carolinianum plants collected from three distinct agroecosystems. The virus was not detected in eight other species of the genus Geranium. There was no association of a particular phenotypic trait of the host with the presence or absence of the virus. GcEV1 was transmitted at a rate of 100% in seeds of a self-pollinated G. carolinianum plant.

Ultrastructural Analysis of Cells From Bell Pepper (Capsicum annuum) Infected With Bell Pepper Endornavirus

Endornaviruses include viruses that infect fungi, oomycetes, and plants. The genome of plant endornaviruses consists of linear ssRNA ranging in size from approximately 13-18 kb and lacking capsid protein and cell-to-cell movement capability. Although, plant endornaviruses have not been shown to cause detectable changes in the plant phenotype, they have been associated with alterations of the host physiology. Except for the association of cytoplasmic vesicles with infections by Vicia faba endornavirus, effects on the plant cell ultrastructure caused by endornaviruses have not been reported. Bell pepper endornavirus (BPEV) has been identified in several pepper (Capsicum spp.) species. We conducted ultrastructural analyses of cells from two near-isogenic lines of the bell pepper (C. annuum) cv. Marengo, one infected with BPEV and the other BPEV-free, and found cellular alterations associated with BPEV-infections. Some cells of plants infected with BPEV exhibited alterations of organelles and other cell components. Affected cells were located mainly in the mesophyll and phloem tissues. Altered organelles included mitochondrion, chloroplast, and nucleus. The mitochondria from BPEV-infected plants exhibited low number of cristae and electron-lucent regions. Chloroplasts contained plastoglobules and small vesicles in the surrounding cytoplasm. Translucent regions in thylakoids were observed, as well as hypertrophy of the chloroplast structure. Many membranous vesicles were observed in the stroma along the envelope. The nuclei revealed a dilation of the nuclear envelope with vesicles and perinuclear areas. The organelle changes were accompanied by membranous structure rearrangements, such as paramural bodies and multivesicular bodies. These alterations were not observed in cells from plants of the BPEV-free line. Overall, the observed ultrastructural cell alterations associated with BPEV are similar to those caused by plant viruses and viroids and suggest some degree of parasitic interaction between BPEV and the plant host.

Complete genome sequence of a novel comovirus infecting common bean

The complete genome sequence of a novel comovirus identified in Guanajuato, Mexico, in a common bean plant (Phaseolus vulgaris L.) coinfected with Phaseolus vulgaris alphaendornavirus 1 (PvEV-1) and Phaseolus vulgaris alphaendornavirus 2 (PvEV-2) is presented. According to the current ICTV taxonomic criteria, this comovirus corresponds to a new species, and the name "Phaseolus vulgaris severe mosaic virus" (PvSMV) is proposed for this virus based on the observed symptoms of "severe mosaic" syndrome caused by comoviruses in common bean. PvSMV is closely related to bean pod mosaic virus (BPMV), and its genome consists of two polyadenylated RNAs. RNA-1 (GenBank accession number MN837498) is 5969 nucleotides (nt) long and encodes a single polyprotein of 1856 amino acids (aa), with an estimated molecular weight (MW) of 210 kDa, that contains putative proteins responsible for viral replication and proteolytic processing. RNA-2 (GenBank accession number MN837499) is 3762 nt long and encodes a single polyprotein of 1024 aa, with an estimated MW of 114 kDa, that contains putative movement and coat proteins. Cleavage sites were predicted based on similarities in size and homology to aa sequences of other comoviruses available in the GenBank database. Symptoms associated with PvSMV include mosaic, local necrotic lesions, and apical necrosis. This is the first report of a comovirus infecting common bean in Mexico.

Viruses Infecting the Plant Pathogenic Fungus Rhizoctonia solani

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.

Viromes in Xylariaceae fungi infecting avocado in Spain

Four isolates of Entoleuca sp., family Xylariaceae, Ascomycota, recovered from avocado rhizosphere in Spain were analyzed for mycoviruses presence. For that, the dsRNAs from the mycelia were extracted and subjected to metagenomics analysis that revealed the presence of eleven viruses putatively belonging to families Partitiviridae, Hypoviridae, Megabirnaviridae, and orders Tymovirales and Bunyavirales, in addition to one ourmia-like virus plus other two unclassified virus species. Moreover, a sequence with 98% nucleotide identity to plant endornavirus Phaseolus vulgaris alphaendornavirus 1 has been identified in the Entoleuca sp. isolates. Concerning the virome composition, the four isolates only differed in the presence of the bunyavirus and the ourmia-like virus, while all other viruses showed common patterns. Specific primers allowed the detection by RT-PCR of these viruses in a collection of Entoleuca sp. and Rosellinia necatrix isolates obtained from roots of avocado trees. Results indicate that intra- and interspecies horizontal virus transmission occur frequently in this pathosystem.

Molecular Characterization of a Novel Endornavirus Conferring Hypovirulence in Rice Sheath Blight Fungus Rhizoctonia solani AG-1 IA Strain GD-2

The complete sequence and genome organization of a novel Endornavirus from the hypovirulent strain GD-2 of Rhizoctonia solani AG-1 IA, the causal agent of rice sheath blight, were identified using a deep sequencing approach and it was tentatively named as Rhizoctonia solani endornavirus 1 (RsEV1). It was composed of only one segment that was 19,936 bp in length and was found to be the longest endornavirus genome that has been reported so far. The RsEV1 genome contained two open reading frames (ORFs): ORF1 and ORF2. ORF1 contained a glycosyltransferase 1 domain and a conserved RNA-dependent RNA polymerase domain, whereas ORF2 encoded a conserved hypothetical protein. Phylogenetic analysis revealed that RsEV1 was phylogenetically a new endogenous RNA virus. A horizontal transmission experiment indicated that RsEV1 could be transmitted from the host fungal strain GD-2 to a virulent strain GD-118P and resulted in hypovirulence in the derivative isogenic strain GD-118P-V1. Metabolomic analysis showed that 32 metabolites were differentially expressed between GD-118P and its isogenic hypovirulent strain GD-118P-V1. The differential metabolites were mainly classified as organic acids, amino acids, carbohydrates, and the intermediate products of energy metabolism. Pathway annotation revealed that these 32 metabolites were mainly involved in pentose and glucuronate interconversions and glyoxylate, dicarboxylate, starch, and sucrose metabolism, and so on. Taken together, our results showed that RsEV1 is a novel Endornavirus, and the infection of virulent strain GD-118P by RsEV1 caused metabolic disorders and resulted in hypovirulence. The results of this study lay a foundation for the biocontrol of rice sheath blight caused by R. solani AG1-IA.

Double-Stranded RNA High-Throughput Sequencing Reveals a New Cytorhabdovirus in a Bean Golden Mosaic Virus-Resistant Common Bean Transgenic Line

Using double-strand RNA (dsRNA) high-throughput sequencing, we identified five RNA viruses in a bean golden mosaic virus (BGMV)-resistant common bean transgenic line with symptoms of viral infection. Four of the identified viruses had already been described as infecting common bean (cowpea mild mottle virus, bean rugose mosaic virus, Phaseolus vulgaris alphaendornavirus 1, and Phaseolus vulgaris alphaendornavirus 2) and one is a putative new plant rhabdovirus (genus Cytorhabdovirus), tentatively named bean-associated cytorhabdovirus (BaCV). The BaCV genome presented all five open reading frames (ORFs) found in most rhabdoviruses: nucleoprotein (N) (ORF1) (451 amino acids, aa), phosphoprotein (P) (ORF2) (445 aa), matrix (M) (ORF4) (287 aa), glycoprotein (G) (ORF5) (520 aa), and an RNA-dependent RNA polymerase (L) (ORF6) (114 aa), as well as a putative movement protein (P3) (ORF3) (189 aa) and the hypothetical small protein P4. The predicted BaCV proteins were compared to homologous proteins from the closest cytorhabdoviruses, and a low level of sequence identity (15⁻39%) was observed. The phylogenetic analysis shows that BaCV clustered with yerba mate chlorosis-associated virus (YmCaV) and rice stripe mosaic virus (RSMV). Overall, our results provide strong evidence that BaCV is indeed a new virus species in the genus Cytorhabdovirus (family Rhabdoviridae), the first rhabdovirus to be identified infecting common bean.

Metagenomic Analysis of Plant Virus Occurrence in Common Bean (Phaseolus vulgaris) in Central Kenya

Two closely related potyviruses, bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV), are regarded as major constraints on production of common bean (Phaseolus vulgaris L.) in Eastern and Central Africa, where this crop provides a high proportion of dietary protein as well as other nutritional, agronomic, and economic benefits. Previous studies using antibody-based assays and indicator plants indicated that BCMV and BCMNV are both prevalent in bean fields in the region but these approaches cannot distinguish between these potyviruses or detect other viruses that may threaten the crop. In this study, we utilized next generation shotgun sequencing for a metagenomic examination of viruses present in bean plants growing at two locations in Kenya: the University of Nairobi Research Farm in Nairobi's Kabete district and at sites in Kirinyaga County. RNA was extracted from leaves of bean plants exhibiting apparent viral symptoms and sequenced on the Illumina MiSeq platform. We detected BCMNV, cucumber mosaic virus (CMV), and Phaseolus vulgaris alphaendornaviruses 1 and 2 (PvEV1 and 2), with CMV present in the Kirinyaga samples. The CMV strain detected in this study was most closely related to Asian strains, which suggests that it may be a recent introduction to the region. Surprisingly, and in contrast to previous surveys, BCMV was not detected in plants at either location. Some plants were infected with PvEV1 and 2. The detection of PvEV1 and 2 suggests these seed transmitted viruses may be more prevalent in Eastern African bean germplasm than previously thought.

Comprehensive Surveys of Bean common mosaic virus and Bean common mosaic necrosis virus and Molecular Evidence for Occurrence of Other Phaseolus vulgaris Viruses in Tanzania

Virus diseases are among the main biotic factors constraining common bean (Phaseolus vulgaris L.) production in Tanzania. Disease management requires information on types, distribution, incidence, and genetic variation of the causal viruses, which is currently limited. Thus, a countrywide comprehensive survey was conducted. Use of a next-generation sequencing technique enabled simultaneous detection of 15 viruses belonging to 11 genera. De novo assembly resulted in many contigs, including complete or nearly complete sequences of Bean common mosaic virus (BCMV), Bean common mosaic necrosis virus (BCMNV), and Southern bean mosaic virus (SBMV). Some viruses (for example, SBMV and Tomato leaf curl Uganda virus-related begomovirus) were detected for the first time in common bean in Tanzania. Visually assessed virus-like disease incidence ranged from 0 to 98% but reverse-transcription polymerase chain reaction-based incidence of BCMV and BCMNV (7,756 samples) was mostly less than 40%. The Sanger-based nucleotide sequences encoding coat proteins of BCMV and BCMNV isolates were 90.2 to 100% and 97.1 to 100% identical to each other, respectively. Phylogenetic analysis showed that BCMV isolates were more diverse than BCMNV isolates. The information generated in this study will contribute to the development of molecular diagnostic tools and strategies for management of virus diseases nationally and internationally. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Sclerotinia minor Endornavirus 1, a Novel Pathogenicity Debilitation-Associated Mycovirus with a Wide Spectrum of Horizontal Transmissibility

Sclerotinia minor is a phytopathogenic fungus causing sclerotinia blight on many economically important crops. Here, we have characterized the biological and molecular properties of a novel endornavirus, Sclerotinia minor endornavirus 1 (SmEV1), isolated from the hypovirulent strain LC22 of S. minor. The genome of SmEV1 is 12,626 bp long with a single, large open reading frame (ORF), coding for a putative protein of 4020 amino acids. The putative protein contains cysteine-rich region (CRR), viral methyltransferase (MTR), putative DEXDc, viral helicase (Hel), and RNA-dependent RNA polymerase (RdRp) domains. The putative protein and the conserved domains are phylogenetically related to endornaviruses. SmEV1 does not contain a site-specific nick characteristic of most previously described endornaviruses. Hypovirulence and associated traits of strain LC22 and SmEV1 were readily cotransmitted horizontally via hyphal contact to isolates of different vegetative compatibility groups of S. minor. Additionally, SmEV1 in strain LC22 was found capable of being transmitted vertically through sclerotia. Furthermore, mycelium fragments of hypovirulent strain LC22 have a protective activity against attack by S. minor. Taken together, we concluded that SmEV1 is a novel hypovirulence-associated mycovirus with a wide spectrum of transmissibility, and has potential for biological control (virocontrol) of diseases caused by S. minor.

Pathogenic seedborne viruses are rare but Phaseolus vulgaris endornaviruses are common in bean varieties grown in Nicaragua and Tanzania

Common bean (Phaseolus vulgaris) is an annual grain legume that was domesticated in Mesoamerica (Central America) and the Andes. It is currently grown widely also on other continents including Africa. We surveyed seedborne viruses in new common bean varieties introduced to Nicaragua (Central America) and in landraces and improved varieties grown in Tanzania (eastern Africa). Bean seeds, harvested from Nicaragua and Tanzania, were grown in insect-controlled greenhouse or screenhouse, respectively, to obtain leaf material for virus testing. Equal amounts of total RNA from different samples were pooled (30-36 samples per pool), and small RNAs were deep-sequenced (Illumina). Assembly of the reads (21-24 nt) to contiguous sequences and searches for homologous viral sequences in databases revealed Phaseolus vulgaris endornavirus 1 (PvEV-1) and PvEV-2 in the bean varieties in Nicaragua and Tanzania. These viruses are not known to cause symptoms in common bean and are considered non-pathogenic. The small-RNA reads from each pool of samples were mapped to the previously characterized complete PvEV-1 and PvEV-2 sequences (genome lengths ca. 14 kb and 15 kb, respectively). Coverage of the viral genomes was 87.9-99.9%, depending on the pool. Coverage per nucleotide ranged from 5 to 471, confirming virus identification. PvEV-1 and PvEV-2 are known to occur in Phaseolus spp. in Central America, but there is little previous information about their occurrence in Nicaragua, and no information about occurrence in Africa. Aside from Cowpea mild mosaic virus detected in bean plants grown from been seeds harvested from one region in Tanzania, no other pathogenic seedborne viruses were detected. The low incidence of infections caused by pathogenic viruses transmitted via bean seeds may be attributable to new, virus-resistant CB varieties released by breeding programs in Nicaragua and Tanzania.

Viruses infecting common bean (Phaseolus vulgaris L.) in Tanzania: A review on molecular characterization, detection and disease management options

Common bean (Phaseolus vulgaris L.) is a major legume crop, serving as a main source of dietary protein and calories and generating income for many Tanzanians. It is produced in nearly all agro-ecological zones of Tanzania. However, the average yields are low (<1000 kg/ha), which is attributed to many factors including virus diseases. The most important viruses of common bean in Tanzania are Bean common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) but other viruses have also been reported. There has never been a review of common bean virus diseases in the country, and the lack of collated information makes their management difficult. Therefore, this review focuses on (1) occurrence of different viruses of common bean in Tanzania, (2) molecular characterization of these viruses, (3) detection tools for common bean viruses in Tanzania and (4) available options for managing virus diseases in the country. Literature and nucleotide sequence database searches revealed that common bean diseases are inadequately studied and that their causal viruses have not been adequately characterized at the molecular level in Tanzania. Increased awareness on common bean virus diseases in Tanzania is expected to result into informed development of strategies for management of the same and thus increased production, which in turn has implication on nutrition and income.

Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control

The majority of plant viruses contain RNA genomes. Detection of viral RNA genomes in infected plant material by next generation sequencing (NGS) is possible through the extraction and sequencing of total RNA, total RNA devoid of ribosomal RNA, small RNA interference (RNAi) molecules, or double stranded RNA (dsRNA). Plants do not typically produce high molecular weight dsRNA, therefore the presence of dsRNA makes it an attractive target for plant virus diagnostics. The sensitivity of NGS as a diagnostic method demands an effective dsRNA protocol that is both representative of the sample and minimizes sample cross contamination. We have developed a modified dsRNA extraction protocol that is more efficient compared to traditional protocols, requiring reduced amounts of starting material, that is less prone to sample cross contamination. This was accomplished by using bead based homogenization of plant material in closed, disposable 50ml tubes. To assess the quality of extraction, we also developed an internal control by designing a real-time (quantitative) PCR (qPCR) assay that targets endornaviruses present in Phaseolus vulgaris cultivar Black Turtle Soup (BTS).

Complete genomic sequence of barley (Hordeum vulgare) endornavirus (HvEV) determined by next-generation sequencing

Endornaviruses are unusual plant-, fungus- and oomycete-infecting viruses with a large, ca 14- to 17-kb linear double-stranded RNA (dsRNA) genome and a persistent lifestyle. The complete genome sequence of an endornavirus from the barley (Hordeum vulgare) Nerz variety was determined from paired Illumina MySeq reads derived from purified dsRNAs. The genome is 14,243 nt long, with 5' and 3' non-coding regions of 207 and 47 nt, respectively. It encodes a single large protein of 4663 amino acids that carries conserved motifs for a methyltransferase, a helicase and an RNA-dependent RNA polymerase. The sequence of Hordeum vulgare endornavirus (HvEV) carries all the hallmarks of a typical member of the genus Endornavirus, with the exception of an UDP-glycosyltransferase motif observed in many, but not all, endornaviral genomes.

Complete Genome Sequence of a Bell Pepper Endornavirus Isolate from Canada

Bell pepper endornavirus (BPEV) is a double-stranded RNA virus infecting economically important crops, such as peppers. Next-generation sequencing of small RNAs extracted from the leaves of a pepper plant showing mild viral symptoms, along with subsequent analysis, identified BPEV. The complete genome of this isolate was cloned and sequenced.

Two endornaviruses show differential infection patterns between gene pools of Phaseolus vulgaris

We investigated the occurrence of two plant endornaviruses, Phaseolus vulgaris endornavirus 1 and Phaseolus vulgaris endornavirus 2, in breeding lines, cultivars, landraces, and wild genotypes of common bean (Phaseolus vulgaris) collected from the two centers of common bean domestication: Mesoamerica and the Andes. The two endornaviruses were detected in many genotypes of Mesoamerican origin but rarely in genotypes of Andean origin. The results suggest that these two endornaviruses were introduced into the Mesoamerican modern genotypes during common bean domestication and provide more evidence for the existence of two divergent gene pools of common bean.

Unique symbiotic viruses in plants: Endornaviruses

Linear double-stranded RNAs (dsRNAs) of about 15 kbp in length are often found from healthy plants, such as bell pepper and rice plants. Nucleotide sequencing and phylogenetic analyses reveal that these dsRNAs are not transcribed from host genomic DNAs, encode a single long open reading frame (ORF) with a viral RNA-dependent RNA polymerase domain, and contain a site-specific nick in the 5' region of their coding strands. Consequently the International Committee on Taxonomy of Viruses has approved that these dsRNAs are viruses forming a distinct taxon, the family Endornaviridae the genus Endornavirus. Endornaviruses have common properties that differ from those of conventional viruses: they have no obvious effect on the phenotype of their host plants, and they are efficiently transmitted to the next generation via both pollen and ova, but their horizontal transfer to other plants has never been proven. Conventional single-stranded RNA viruses, such as cucumber mosaic virus, propagate hugely and systemically in host plants to sometime kill their hosts eventually and transmit horizontally (infect to other plants). In contrast, copy numbers of endornaviruses are low and constant (about 100 copies/cell), and they symbiotically propagate with host plants and transmit vertically. Therefore, endornaviruses are unique plant viruses with symbiotic properties.

Molecular characterisation of an endornavirus from Rhizoctonia solani AG-3PT infecting potato

Rhizoctonia solani (teleomorph: Thanatephorus cucumeris) is a soil-borne plant pathogenic fungus that has a broad host range, including potato. In this study, the double-stranded RNA (dsRNA) profiles were defined for 39 Rhizoctonia solani isolates representative of two different anastomosis groups (AGs) associated with black scurf of potato in New Zealand. A large dsRNA of c. 12 kb-18 kb was detected in each of the isolates, regardless of AG or virulence on potato. Characterisation of the large dsRNA from R. solani AG-3PT isolate RS002, using random amplification of total dsRNA and analyses of overlapping cDNA sequences, resulted in the assembly of a consensus sequence of 14 694 nt. A single, large open reading frame was identified on the positive strand of the assembled sequence encoding a putative polypeptide of at least 4893 amino acids, with a predicted molecular mass of 555.6 kDa. Conserved domains within this polypeptide included those for a viral methyltransferase, a viral RNA helicase 1 and an RNA-dependent RNA polymerase. The domains and their sequential organisation revealed the polyprotein was very similar to those encoded by dsRNA viruses of the genus Endornavirus, in the family Endornaviridae. This is the first report of an endornavirus in R. solani, and thus the putative virus is herein named Rhizoctonia solani endornavirus - RS002 (RsEV-RS002). Partial characterisation of the large dsRNAs in five additional AG-3PT isolates of R. solani also identified them as probable endornaviruses, suggesting this family of viruses is widespread in R. solani infecting potato. The ubiquitous nature of endornaviruses in this plant pathogen implies they may have an important, but yet uncharacterised, role in R. solani.

A new endornavirus species infecting Malabar spinach (Basella alba L.)

A putative new endornavirus was isolated from Malabar spinach (Basella alba). The viral dsRNA consisted of 14,027 nt with a single ORF that coded for a polyprotein of 4,508 aa. The genome organization was similar to that of four other endornaviruses. Conserved domains for helicase-1, capsular synthase, UDP-glucose-glycosyltransferase (UGT), and RdRp were detected. Infected plants were phenotypically undistinguishable from healthy ones. The name Basella alba endornavirus is proposed for the virus isolated from Malabar spinach.

Molecular characterisation of an endornavirus infecting the phytopathogen Sclerotinia sclerotiorum

The complete sequence and genome organisation of an endornavirus from the phytopathogenic fungus Sclerotinia sclerotiorum isolate 11691 was described and the name Sclerotinia sclerotiorum endornavirus 1 (SsEV1/11691) proposed. The genome is 10,513 nucleotides (nts) long with a single open reading frame (ORF) that codes for a single polyprotein of 3459 amino acid (aa) residues. The polyprotein contains cysteine-rich region (CRR), viral methyltransferase (MTR), putative DEXDc, viral helicase (Hel), phytoreo_S7 (S7) and RNA-dependent RNA polymerase (RdRp) domains. The polyprotein and the conserved domains are phylogenetically related to endornaviruses. However, the coding strand of SsEV1/11691 does not contain a site-specific nick characteristic of most previously described endornaviruses. The elimination of SsEV1/11691 did not result in any significant changes in the host phenotype and virulence.

Complete nucleotide sequence and genome organization of an endornavirus from bottle gourd (Lagenaria siceraria) in California, U.S.A

The full-length nucleotide sequence and genome organization of an Endornavirus isolated from ornamental hard shell bottle gourd plants (Lagenaria siceraria (Molina) Standl.) in California (CA), USA tentatively named L. siceraria endornavirus-California (LsEV-CA) was determined. The LsEV-CA genome was 15088 bp in length, with a G + C content of 36.55 %. The lengths of the 5' and 3' untranslated regions were 111 and 52 bp, respectively. The genome of LsEV-CA contained one large ORF encoding a 576 kDa polyprotein. The predicted protein contains two glycosyltransferase motifs, as well as RNA-dependent RNA polymerase and helicase domains. LsEV-CA was detected in healthy-looking field-grown gourd plants, as well as plants expressing yellows symptoms. It was also detected in non-symptomatic greenhouse-grown gourd seedlings grown from seed obtained from the same field sites. These preliminary data indicate that LsEV-CA is likely not associated with the gourd-yellows syndrome observed in the field.