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

Herschlag, Rachel; Okada, Ryo; Alcalá-Briseño, Ricardo I.; Souto, Eliezer Rodrigues de; Valverde, R. A.

doi:10.1016/j.virusres.2020.198116

Cited by 4 publications

(6 citation statements)

References 48 publications

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“…In 2021, Li et al [5] presented a detailed phylogeny for the RdRP domains of endornaviruses and demonstrated a basal position of the PvEV-3/GcEV-1 clade to all other alphaendornavirus clades, albeit not proposing a new taxonomic unit. Our phylogeny for the HEL domain of endornaviruses (Figure 3b) complements the previously available phylogenetic trees for RdRP domains [5,28,41] and provides an additional argument for the creation of a third genus in the family Endornaviridae, which we propose to name the genus Gammaendornavirus. Incidentally, the name Gammaendornavirus was proposed for a phylogroup within the genus Alphaendornavirus earlier [42], but the proposal was based on an RdRP phylogeny only and for a relatively small number of endornavirus sequences available at the time; this proposal was later rejected [5].…”

Section: Discussionsupporting

confidence: 66%

“…The close RdRP phylogenetic placement has been noted for PvEV-3 and GcEV-1 before [5,28,41]. In 2021, Li et al [5] presented a detailed phylogeny for the RdRP domains of endornaviruses and demonstrated a basal position of the PvEV-3/GcEV-1 clade to all other alphaendornavirus clades, albeit not proposing a new taxonomic unit.…”

Section: Discussionmentioning

confidence: 91%

“…The phylogenetic trees for the HEL and RdRP proteins were generated based on the set of sequences provided in a report by the International Committee on Taxonomy of Viruses (ICTV) on the family Endornaviridae [ 3 , 4 ], with the addition of GEV-1, GEV-2, and GEEV-Ch (this work) and the Geranium carolinianum endornavirus 1 sequences (GcEV1) [ 28 ]. The grapevine leafroll-associated virus 1 reference sequence was used as an outgroup.…”

Section: Methodsmentioning

confidence: 99%

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Grapevine Endophyte Endornavirus and Two New Endornaviruses Found Associated with Grapevines (Vitis vinifera L.) in Idaho, USA

Dahan

Orellana

Lee

et al. 2023

Viruses

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Five virus genomes, ranging between 12.0 and 12.3 kb in length and identified as endornaviruses, were discovered through a high-throughput sequencing (HTS) analysis of the total RNA samples extracted from two wine grape cultivars collected in the state of Idaho. One was found in a declining Chardonnay vine and was determined to be a local isolate of grapevine endophyte endornavirus (GEEV), and four others represented two novel endornaviruses named grapevine endornavirus 1 (GEV1) and grapevine endornavirus 2 (GEV2). All three virus genomes span a large, single open reading frame encoding polyproteins with easily identifiable helicase (HEL) and RNA-dependent RNA polymerase (RdRP) domains, while the GEV2 polyprotein also contains a glycosyltransferase domain. The GEV1 genome found in an asymptomatic Cabernet franc vine was related to, but distinct from, GEEV: the 5′-proximal, 4.7 kb segment of the GEV1 genome had a 72% identical nucleotide sequence to that of GEEV, while the rest of the genome displayed no significant similarity to the GEEV nucleotide sequence. Nevertheless, the amino acid sequence of the RdRP domain of GEV1 exhibited the closest affinity to the RdRP of GEEV. GEV2 was found in declining Chardonnay and asymptomatic Cabernet franc vines as three genetic variants exhibiting a 91.9–99.8% nucleotide sequence identity among each other; its RdRP had the closest affinity to the Shahe endorna-like virus 1 found in termites. In phylogenetic analyses, the RdRP and HEL domains of the GEV1 and GEV2 polyproteins were placed in two separate clades inside the large lineage of alphaendornaviruses, showing an affinity to GEEV and Phaseolus vulgaris endornavirus 1, respectively.

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Section: Discussionsupporting

confidence: 66%

Section: Discussionmentioning

confidence: 91%

Section: Methodsmentioning

confidence: 99%

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Grapevine Endophyte Endornavirus and Two New Endornaviruses Found Associated with Grapevines (Vitis vinifera L.) in Idaho, USA

Dahan

Orellana

Lee

et al. 2023

Viruses

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“…Endornaviruses are usually not associated with hypovirulence and do not affect the phenotype of their host [ 6 , 51 , 52 ]. However, so far, more and more endornaviruses with biocontrol potential have been reported.…”

Section: Discussionmentioning

confidence: 99%

Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

Luo

Xiè

Jia

et al. 2022

Viruses

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Endornaviruses are capsidless linear (+) ssRNA viruses in the family Endornaviridae. In this study, Scelrotinia sclerotiorum endornavirus 11 (SsEV11), a novel endornavirus infecting hypovirulent Sclerotinia sclerotiorum strain XY79, was identified and cloned using virome sequencing analysis and rapid amplification of cDNA ends (RACE) techniques. The full-length genome of SsEV11 is 11906 nt in length with a large ORF, which encodes a large polyprotein of 3928 amino acid residues, containing a viral methyltransferase domain, a cysteine-rich region, a putative DEADc, a viral helicase domain, and an RNA-dependent RNA polymerase (RdRp) 2 domain. The 5’ and 3’ untranslated regions (UTR) are 31 nt and 90 nt, respectively. According to the BLAST result of the nucleotide sequence, SsEV11 shows the highest identity (45%) with Sclerotinia minor endornavirus 1 (SmEV1). Phylogenetic analysis based on amino acid sequence of RdRp demonstrated that SsEV11 clusters to endornavirus and has a close relationship with Betaendornavirus. Phylogenetic analysis based on the sequence of endornaviral RdRp domain indicated that there were three large clusters in the phylogenetic tree. Combining the results of alignment analysis, Cluster I at least has five subclusters including typical members of Alphaendornavirus and many unclassified endornaviruses that isolated from fungi, oomycetes, algae, and insects; Cluster II also has five subclusters including typical members of Betaendornavirus, SsEV11, and other unclassified viruses that infected fungi; Cluster III includes many endorna-like viruses that infect nematodes, mites, and insects. Viruses in Cluster I and Cluster II are close to each other and relatively distant to those in Cluster III. Our study characterized a novel betaendornavirus, SsEV11, infected fungal pathogen S. sclerotiorum, and suggested that notable phylogenetic diverse exists in endornaviruses. In addition, at least, one novel genus, Gammaendornavirus, should be established to accommodate those endorna-like viruses in Cluster III.

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“…Given these characteristics, understanding the evolution and epidemiology of endornaviruses is of great interest ( Song et al., 2013 ; Roossinck et al., 2010 , 2011 ; Fukuhara et al., 2019 ). However, only a limited number of potential hosts have been investigated for the presence of endornaviruses, and the host range, genetic diversity, and geographic distribution of the majority of endornaviruses, especially those from fungi, remain poorly characterized ( Okada et al., 2011 ; Sabanadzovic et al., 2016 , 2018 ; Herschlag et al., 2020 ).…”

mentioning

confidence: 99%

Four closely related endornaviruses each with a low incidence in the phytopathogenic fungi Exserohilum turcicum or Bipolaris maydis

Wang,

Pan,

Zheng

et al. 2024

Virus Research

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

Cited by 4 publications

References 48 publications

Grapevine Endophyte Endornavirus and Two New Endornaviruses Found Associated with Grapevines (Vitis vinifera L.) in Idaho, USA

Grapevine Endophyte Endornavirus and Two New Endornaviruses Found Associated with Grapevines (Vitis vinifera L.) in Idaho, USA

Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

Four closely related endornaviruses each with a low incidence in the phytopathogenic fungi Exserohilum turcicum or Bipolaris maydis

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