A new virus of the family Tombusviridae infecting sugarcane

Tahir, Muhammad Nouman; Bolus, Stephen; Grinstead, Samuel; McFarlane, S. A.; Mollov, Dimitre

doi:10.1007/s00705-020-04908-9

Cited by 17 publications

(9 citation statements)

References 12 publications

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“…Another 3′ CITE that is prevalent in umbraviruses (the BTE) also shares no sequence or structural similarity with Structure 14 [65]. The reported SULV sequence terminates within this 3′ CITE and thus the sequence appears to be truncated and not full-length as reported [20]. Structure 14 and all of its conserved sequences are absent in Class 1 and Class 3 ulaRNAs.…”

Section: Features Of Domain 3: Structure 14mentioning

confidence: 79%

“…Although a virus with sequence similarity to poleroviruses was found in aphids feeding on the opuntia plants, no evidence for this virus was found in opuntia containing OULV [17]. Similar ulaRNAs sequences from sugarcane (sugarcane umbra-like virus; SULV) [20] and citrus (citrus yellow vein associated virus; CYVaV) (Kwon et al, submitted) have been reported, and additional sequences from Ethiopian maize (Ethiopian maize associated virus; EMaV) and strawberry (strawberry associated virus A; SbaVA) have been deposited in GenBank (Figure 1).…”

Section: Introductionmentioning

confidence: 99%

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Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs

Liu

Carino

Bera

et al. 2021

Viruses

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We report the biological and structural characterization of umbravirus-like associated RNAs (ulaRNAs), a new category of coat-protein dependent subviral RNA replicons that infect plants. These RNAs encode an RNA-dependent RNA polymerase (RdRp) following a −1 ribosomal frameshift event, are 2.7–4.6 kb in length, and are related to umbraviruses, unlike similar RNA replicons that are related to tombusviruses. Three classes of ulaRNAs are proposed, with citrus yellow vein associated virus (CYVaV) placed in Class 2. With the exception of CYVaV, Class 2 and Class 3 ulaRNAs encode an additional open reading frame (ORF) with movement protein-like motifs made possible by additional sequences just past the RdRp termination codon. The full-length secondary structure of CYVaV was determined using Selective 2’ Hydroxyl Acylation analyzed by Primer Extension (SHAPE) structure probing and phylogenic comparisons, which was used as a template for determining the putative structures of the other Class 2 ulaRNAs, revealing a number of distinctive structural features. The ribosome recoding sites of nearly all ulaRNAs, which differ significantly from those of umbraviruses, may exist in two conformations and are highly efficient. The 3′ regions of Class 2 and Class 3 ulaRNAs have structural elements similar to those of nearly all umbraviruses, and all Class 2 ulaRNAs have a unique, conserved 3′ cap-independent translation enhancer. CYVaV replicates independently in protoplasts, demonstrating that the reported sequence is full-length. Additionally, CYVaV contains a sequence in its 3′ UTR that confers protection to nonsense mediated decay (NMD), thus likely obviating the need for umbravirus ORF3, a known suppressor of NMD. This initial characterization lays down a road map for future investigations into these novel virus-like RNAs.

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Section: Features Of Domain 3: Structure 14mentioning

confidence: 79%

Section: Introductionmentioning

confidence: 99%

Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs

Liu

Carino

Bera

et al. 2021

Viruses

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“…Recent studies on various plant hosts, reported small viruses and virus-associated RNAs of approximately 2.8–4.5 kb in size containing two or more ORFs ( Mo et al, 2011 ; Quito-Avila et al, 2015 ; Sa Antunes et al, 2016 ; Felker et al, 2019 ; Campbell et al, 2020 ; Yoshida, 2020 ; Tahir et al, 2021 ). CYVaV has been referenced by many of these reports to be related to such small virus-like RNAs ( Quito-Avila et al, 2015 ; Sa Antunes et al, 2016 ; Tahir et al, 2021 ). However, CYVaV remains distinct among them because of the smaller size (approximately 2.7 kb) and organization of its genome and putative expression mechanism of its two ORFs (−1 ribosomal frameshift; Figure 2 ) as well as the low aa sequence similarity of its ORF1 encoded protein and RdRp (i.e., <74%).…”

Section: Discussionmentioning

confidence: 99%

Complete Nucleotide Sequence, Genome Organization, and Comparative Genomic Analyses of Citrus Yellow-Vein Associated Virus (CYVaV)

et al. 2021

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Citrus yellow-vein disease (CYVD) was first reported in California in 1957. We now report that CYVD is associated with a virus-like agent, provisionally named citrus yellow-vein associated virus (CYVaV). The CYVaV RNA genome has 2,692 nucleotides and codes for two discernable open reading frames (ORFs). ORF1 encodes a protein of 190 amino acid (aa) whereas ORF2 is presumably generated by a −1 ribosomal frameshifting event just upstream of the ORF1 termination signal. The frameshift product (717 aa) encodes the RNA-dependent RNA polymerase (RdRp). Phylogenetic analyses suggest that CYVaV is closely related to unclassified virus-like RNAs in the family Tombusviridae. Bio-indexing and RNA-seq experiments indicate that CYVaV can induce yellow vein symptoms independently of known citrus viruses or viroids.

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“…Umbraviruses and unclassified umbra-like viruses were the final viruses shared by quarantined sugarcane and wild Poaceae. Umbra-like viruses, which are similar to umbraviruses but do not contain all of the umbravirus genomic features [ 9 ], have been previously found in sugarcane in Florida [ 7 ] and South Africa [ 9 ]. Umbra-like virus sequences have, so far, not been reported in other Poaceae with the exception of Ethiopia-maize-associated virus that was initially considered as an unclassified virus [ 52 ].…”

Section: Discussionmentioning

confidence: 99%

“…Viruses are the most detected pathogens in sugarcane quarantine [ 3 , 4 ]. Imported planting material can host viruses [ 4 , 5 , 6 ] that are either known for damaging sugarcane crops (the overall majority of sugarcane mastreviruses, poaceviruses, poleroviruses, and potyviruses) or whose effect on sugarcane growth is unknown (ampeloviruses, badnaviruses, and at least one umbravirus and one mastrevirus) [ 4 , 6 , 7 , 8 , 9 ]. On the other hand, plant viruses occurring in Poaceae growing around a quarantine glasshouse are usually unknown.…”

Section: Introductionmentioning

confidence: 99%

Comparison of the Virome of Quarantined Sugarcane Varieties and the Virome of Grasses Growing near the Quarantine Station

Daugrois

Julian

Claude

et al. 2021

Viruses

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Visacane is a sugarcane quarantine station located in the South of France, far away from sugarcane growing areas. Visacane imports up to 100 sugarcane varieties per year, using safe control and confinement measures of plants and their wastes to prevent any risk of pathogen spread outside of the facilities. Viruses hosted by the imported material are either known or unknown to cause disease in cultivated sugarcane. Poaceae viruses occurring in plants surrounding the quarantine glasshouse are currently unknown. These viruses could be considered as a source of new sugarcane infections and potentially cause new sugarcane diseases in cases of confinement barrier failure. The aim of this study was to compare the plant virome inside and outside of the quarantine station to identify potential confinement failures and risks of cross infections. Leaves from quarantined sugarcane varieties and from wild Poaceae growing near the quarantine were collected and processed by a metagenomics approach based on virion-associated nucleic acids extraction and library preparation for Illumina sequencing. While viruses belonging to the same virus genus or family were identified in the sugarcane quarantine and its surroundings, no virus species was detected in both environments. Based on the data obtained in this study, no virus movement between quarantined sugarcane and nearby grassland has occurred so far, and the confinement procedures of Visacane appear to be properly implemented.

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A new virus of the family Tombusviridae infecting sugarcane

Cited by 17 publications

References 12 publications

Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs

Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs

Complete Nucleotide Sequence, Genome Organization, and Comparative Genomic Analyses of Citrus Yellow-Vein Associated Virus (CYVaV)

Comparison of the Virome of Quarantined Sugarcane Varieties and the Virome of Grasses Growing near the Quarantine Station

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