scholarly journals A Virus in American Blackcurrant (Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 406 ◽  
Author(s):  
Thanuja Thekke-Veetil ◽  
Thien Ho ◽  
Joseph Postman ◽  
Robert Martin ◽  
Ioannis Tzanetakis
Keyword(s):  
Genome Organization ◽  
High Throughput Sequencing ◽  
Triple Gene Block ◽  
Open Reading Frames ◽  
Methyl Transferase ◽  
Gene Block ◽  
New Family ◽  
Molecular Features ◽  
Genome Features ◽  
Novel Virus

A novel virus with distinct genome features was discovered by high throughput sequencing in a symptomatic blackcurrant plant. The virus, tentatively named Ribes americanum virus A (RAVA), has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames were identified, with the first encoding a putative viral replicase with methyl transferase (MTR), AlkB, helicase, and RNA dependent RNA polymerase (RdRp) domains. The genome organization downstream of the replicase resembles that of members of the order Tymovirales with an unconventional triple gene block (TGB) movement protein arrangement with none of the other four putative proteins exhibiting significant homology to viral proteins. Phylogenetic analysis using replicase conserved motifs loosely placed RAVA within the Betaflexiviridae. Data strongly suggest that RAVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family within the order Tymovirales.

scholarly journals A Virus in American Blackcurrant (Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales

2018 ◽  
Author(s):  
Thanuja Thekke-Veetil ◽  
Thien Ho ◽  
Joseph D. Postman ◽  
Robert R. Martin ◽  
Ioannis E. Tzanetakis
Keyword(s):  
Genome Organization ◽  
High Throughput Sequencing ◽  
Triple Gene Block ◽  
Open Reading Frames ◽  
Methyl Transferase ◽  
Gene Block ◽  
New Family ◽  
Molecular Features ◽  
Genome Features ◽  
Novel Virus

A novel virus with distinct genome features was discovered by high throughput sequencing in a symptomatic blackcurrant plant. The virus tentatively named as blackcurrant virus A (BCVA) has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames were identified with the first encoding a putative viral replicase with methyl transferase (MTR), AlkB, helicase and RNA dependent RNA polymerase (RdRp) domains. The other four putative proteins exhibit no significant homology to other virus proteins. The genome organization downstream of the replicase resembles that of members of the order Tymovirales with an unconventional triple gene block (TGB) movement protein arrangement. Phylogenetic analysis using replicase conserved motifs loosely placed BCVA within the Betaflexiviridae whereas it was evolutionarily distant to existing members of the family when using the putative TGBp 1-like and coat protein sequences. Our analysis strongly suggests that BCVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family in the order Tymovirales.

scholarly journals Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing

Plants ◽  
2019 ◽  
Vol 8 (6) ◽  
pp. 167 ◽  
Author(s):  
Gonçalo Silva ◽  
Moritz Bömer ◽  
Ajith I. Rathnayake ◽  
Steven O. Sewe ◽  
Paul Visendi ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Triple Gene Block ◽  
Open Reading Frames ◽  
Virus Species ◽  
Gene Block ◽  
Full Diversity ◽  
Putative Coat Protein ◽  
The Family ◽  
International Distribution

To date, several viruses of different genera have been reported to infect yam (Dioscorea spp.). The full diversity of viruses infecting yam, however, remains to be explored. High-throughput sequencing (HTS) methods are increasingly being used in the discovery of new plant viral genomes. In this study, we employed HTS on yam to determine whether any undiscovered viruses were present that would restrict the international distribution of yam germplasm. We discovered a new virus sequence present in 31 yam samples tested and have tentatively named this virus “yam virus Y” (YVY). Twenty-three of the samples in which YVY was detected showed mosaic and chlorotic leaf symptoms, but Yam mosaic virus was also detected in these samples. Complete genome sequences of two YVY viral isolates were assembled and found to contain five open reading frames (ORFs). ORF1 encodes a large replication-associated protein, ORF2, ORF3 and ORF4 constitute the putative triple gene block proteins, and ORF5 encodes a putative coat protein. Considering the species demarcation criteria of the family Betaflexiviridae, YVY should be considered as a novel virus species in the family Betaflexiviridae. Further work is needed to understand the association of this new virus with any symptoms and yield loss and its implication on virus-free seed yam production.

scholarly journals Molecular Characterization of a Novel Wheat-infecting Virus in Family Betaflexiviridae

2021 ◽  
Author(s):  
Jianxiang Wu ◽  
Shuai Fu ◽  
Mengzhu He ◽  
Bingjian Sun ◽  
Xueping Zhou
Keyword(s):  
Triple Gene Block ◽  
International Committee ◽  
Open Reading Frames ◽  
Yellow Mosaic Virus ◽  
Wheat Yellow Mosaic Virus ◽  
Gene Block ◽  
Transmission Electron ◽  
The Family ◽  
Novel Virus

Abstract Wheat plants showing yellow mosaic in leaves and stunting were observed and collected from wheat fields in the Henan Province, China. Analyses of these plants through transmission electron microscopy showed that these plants contained two filamentous virus-like particles of 200–500 nm and 1000–1300 nm long, respectively. RNA-seq result unveiled a co-infection of wheat yellow mosaic virus (WYMV) and an unknown wheat-infecting virus. The complete genome sequence of the unknown virus is 8,410 nucleotide long, excluding its 3’ end poly (A) tail. This unknown virus has six open reading frames (ORFs). The ORF1 encodes a putative viral replication-associated protein, and the ORF2, 3 and 4 encode the triple gene block (TGB) proteins. The ORF5 and 6 encode the capsid protein (CP) and a protein with unknown function, respectively. Phylogenetic relationship analyses showed that this novel virus is evolutionarily related to viruses in the subfamily Quinvirinae, family Betaflexiviridae. It is, however, distinctly different from the viruses in other genera. Based on the species and genus demarcation criteria set by the International Committee on Taxonomy of Viruses (ICTV), we tentatively name this novel virus as wheat yellow stunt-associated betaflexivirus (WYSaBV). We also propose WYSaBV as a new member in a new genus in the family Betaflexiviridae.

scholarly journals The Potato Virus X TGBp2 Protein Plays Dual Functional Roles in Viral Replication and Movement

2018 ◽  
Vol 93 (5) ◽  
Author(s):  
Xiaoyun Wu ◽  
Jiahui Liu ◽  
Mengzhu Chai ◽  
Jinhui Wang ◽  
Dalong Li ◽  
...  
Keyword(s):  
Triple Gene Block ◽  
Potato Virus X ◽  
Plant Viruses ◽  
Open Reading Frames ◽  
Movement Proteins ◽  
Gene Block ◽  
Functional Roles ◽  
Viral Rdrp ◽  
Dual Functional ◽  
Intercellular Movement

ABSTRACTPlant viruses usually encode one or more movement proteins (MP) to accomplish their intercellular movement. A group of positive-strand RNA plant viruses requires three viral proteins (TGBp1, TGBp2, and TGBp3) that are encoded by an evolutionarily conserved genetic module of three partially overlapping open reading frames (ORFs), termed the triple gene block (TGB). However, how these three viral movement proteins function cooperatively in viral intercellular movement is still elusive. Using a novelin vivodouble-stranded RNA (dsRNA) labeling system, we showed that the dsRNAs generated by potato virus X (PVX) RNA-dependent RNA polymerase (RdRp) are colocalized with viral RdRp, which are further tightly covered by “chain mail”-like TGBp2 aggregates and localizes alongside TGBp3 aggregates. We also discovered that TGBp2 interacts with the C-terminal domain of PVX RdRp, and this interaction is required for the localization of TGBp3 and itself to the RdRp/dsRNA bodies. Moreover, we reveal that the central and C-terminal hydrophilic domains of TGBp2 are required to interact with viral RdRp. Finally, we demonstrate that knockout of the entire TGBp2 or the domain involved in interacting with viral RdRp attenuates both PVX replication and movement. Collectively, these findings suggest that TGBp2 plays dual functional roles in PVX replication and intercellular movement.IMPORTANCEMany plant viruses contain three partially overlapping open reading frames (ORFs), termed the triple gene block (TGB), for intercellular movement. However, how the corresponding three proteins coordinate their functions remains obscure. In the present study, we provided multiple lines of evidence supporting the notion that PVX TGBp2 functions as the molecular adaptor bridging the interaction between the RdRp/dsRNA body and TGBp3 by forming “chain mail”-like structures in the RdRp/dsRNA body, which can also enhance viral replication. Taken together, our results provide new insights into the replication and movement of PVX and possibly also other TGB-containing plant viruses.

scholarly journals Discovery and Survey of a New Mandarivirus Associated with Leaf Yellow Mottle Disease of Citrus in Pakistan

Plant Disease ◽  
2020 ◽  
Vol 104 (6) ◽  
pp. 1593-1600 ◽  
Author(s):  
Jiaxing Wu ◽  
Song Zhang ◽  
Sagheer Atta ◽  
Caixia Yang ◽  
Yan Zhou ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Biological Data ◽  
High Sequence Identity ◽  
Reverse Transcription Pcr ◽  
Punjab Province ◽  
Transmission Electron ◽  
Genome Features ◽  
Yellow Mottle ◽  
Novel Virus ◽  
Citrus Trees

During biological indexing for viruses in citrus trees, in a collection of Symons sweet orange (SSO) (Citrus sinensis L. Osbeck) graft inoculated with bark tissues of citrus trees from the Punjab Province in Pakistan, several SSO trees exhibited leaf symptoms of vein yellowing and mottle. High-throughput sequencing by Illumina of RNA preparation depleted of ribosomal RNAs from one symptomatic tree, followed by BLAST analyses, allowed identification of a novel virus, tentatively named citrus yellow mottle-associated virus (CiYMaV). Genome features of CiYMaV are typical of members of the genus Mandarivirus (family Alphaflexiviridae). Virus particles with elongated flexuous shape and size resembling those of mandariviruses were observed by transmission electron microscopy. The proteins encoded by CiYMaV share high sequence identity, conserved motifs, and phylogenetic relationships with the corresponding proteins encoded by Indian citrus ringspot virus (ICRSV) and citrus yellow vein clearing virus (CYVCV), the two current members of the genus Mandarivirus. Although CYVCV is the virus most closely related to CiYMaV, the two viruses can be serologically and biologically discriminated from each other. A reverse-transcription PCR method designed to specifically detect CiYMaV revealed high prevalence (62%) of this virus in 120 citrus trees from the Punjab Province, Pakistan, where the novel virus was found mainly in mixed infection with CYVCV and citrus tristeza virus. However, a preliminary survey on samples from 200 citrus trees from the Yunnan Province, China failed to detect CiYMaV in this region, suggesting that the molecular, serological, and biological data provided here are timely and can help to prevent the spread of this virus in citrus-producing countries.

Small RNA and transcriptome sequencing of a symptomatic peony plant reveals mixed infections with novel viruses

Plant Disease ◽  
2021 ◽  
Author(s):  
Anning Jia ◽  
Chenge Yan ◽  
Hang Yin ◽  
Rui Sun ◽  
Fei Xia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Viral Infections ◽  
Triple Gene Block ◽  
Field Investigation ◽  
Mixed Infections ◽  
Species Classification ◽  
Gene Block ◽  
Sequence Identity

To identify the viruses in tree peony plants associated with the symptoms of yellowing, leaf rolling, stunted growth, and decline, high-throughput sequencing of small RNA and mRNA was conducted from a single symptomatic plant. Bioinformatic analyses and reconstruction of viral genomes indicated mixed viral infections involving cycas necrotic stunt virus (CNSV), apple stem grooving virus (ASGV), lychnis mottle virus (LycMoV), grapevine line pattern virus (GLPV), and three new viruses designated as peony yellowing-associated citrivirus (PYaCV, Citrivirus in Betaflexiviridae), peony betaflexivirus 1 (PeV1, unclassified in Betaflexiviridae), and peony leafroll-associated virus (PLRaV, Ampelovirus in Closteroviridae). PYaCV was 8,666 nucleaotides (nt) in length, comprising three open reading frames (ORFs) and shared 63.8–75.9% nucleotide sequence identity with citrus leaf blotch virus (CLBV) isolates. However, the ORF encoding the replication-associated protein (REP) shared 57% and 52% sequence identities at the nt and amino acid (aa) level, respectively, with other reported CLBV isolates, which were below the criterion for species classification within the family Betaflexiviridae. Recombination analysis identified putative recombination sites in PYaCV, which originated from CLBV. PeV1, only identified from the transcriptome data, was 8,124 nt in length with five ORFs encoding the REP (ORF1), triple gene block (TGB, ORF2–4) and coat protein (CP, ORF5) proteins. Phylogenetic analysis and sequence comparison showed that PeV1 clustered with an unassigned member, the garlic yellow mosaic-associated virus (GYMaV) within the Betaflexiviridae family, into a separate clade. Partial genome sequence analysis of PLRaV (12,545 nt) showed it contained seven ORFs encoding the partial polyprotein 1a, the RNA-dependent RNA polymerase (RdRp), two small hydrophobic proteins p11 and p6, HSP70h, p55, and a CP duplicate, which shared low aa sequence identity with Closteroviridae family members. Phylogenetic analysis based on the aa sequences of RdRp or HSP70h indicated that PLRaV clustered with grapevine leafroll-associated virus 1 (GLRaV-1) and GLRaV-13 in the Ampelovirus genus. Field investigation confirmed the wide distribution of these viruses, causing mixed infections of peony plants in Beijing.

scholarly journals Genomic Analyses of Cherry Rusty Mottle Group and Cherry Twisted Leaf-Associated Viruses Reveal a Possible New Genus Within the FamilyBetaflexiviridae

2015 ◽  
Vol 105 (3) ◽  
pp. 399-408 ◽  
Author(s):  
D. E. V. Villamor ◽  
J. Susaimuthu ◽  
K. C. Eastwell
Keyword(s):  
New Genus ◽  
High Throughput Sequencing ◽  
Prunus Avium ◽  
Triple Gene Block ◽  
Mottle Virus ◽  
Virus Species ◽  
Gene Block ◽  
Green Ring ◽  
The Family ◽  
Prunus Spp

It is demonstrated that closely related viruses within the family Betaflexiviridae are associated with a number of diseases that affect sweet cherry (Prunus avium) and other Prunus spp. Cherry rusty mottle-associated virus (CRMaV) is correlated with the appearance of cherry rusty mottle disease (CRMD), and Cherry twisted leaf-associated virus (CTLaV) is linked to cherry twisted leaf disease (CTLD) and apricot ringpox disease (ARPD). Comprehensive analysis of previously reported full genomic sequences plus those determined in this study representing isolates of CTLaV, CRMaV, Cherry green ring mottle virus, and Cherry necrotic rusty mottle virus revealed segregation of sequences into four clades corresponding to distinct virus species. High-throughput sequencing of RNA from representative source trees for CRMD, CTLD, and ARPD did not reveal additional unique virus sequences that might be associated with these diseases, thereby further substantiating the association of CRMaV and CTLaV with CRMD and CTLD or ARPD, respectively. Based on comparison of the nucleotide and amino acid sequence identity values, phylogenetic relationships with other triple-gene block-coding viruses within the family Betaflexiviridae, genome organization, and natural host range, a new genus (Robigovirus) is suggested.

scholarly journals Cell-to-Cell Movement of Potato virus X: The Role of p12 and p8 Encoded by the Second and Third Open Reading Frames of the Triple Gene Block

2001 ◽  
Vol 14 (10) ◽  
pp. 1158-1167 ◽  
Author(s):  
Atsushi Tamai ◽  
Tetsuo Meshi
Keyword(s):  
Potato Virus ◽  
Fluorescent Protein ◽  
Microprojectile Bombardment ◽  
Triple Gene Block ◽  
Cell Movement ◽  
Potato Virus X ◽  
Open Reading Frames ◽  
Gene Block ◽  
Infected Cells ◽  
Green Fluorescent

Potato virus X (PVX) requires three proteins, p25, p12, and p8, encoded by the triple gene block plus the coat protein (CP) for cell-to-cell movement. When each of these proteins was co-expressed with a cytosolic green fluorescent protein (GFP) in the epidermal cells of Nicotiana benthamiana by the microprojectile bombardment-mediated gene delivery method, only p12 enhanced diffusion of co-expressed GFP, indicating an ability to alter plasmodesmal permeability. p25, p12, and CP, expressed transiently in the initially infected cells, transcomplemented the corresponding movement-defective mutants to spread through two or more cell boundaries. Thus, these proteins probably move from cell to cell with the genomic RNA. In contrast, p8 only functioned intracellularly and was not absolutely required for cell-to-cell movement. Since overexpression of p12 overcame the p8 deficiency, p8 appears to facilitate the functioning of p12, presumably by mediating its intracellular trafficking. Considering the likelihood that p12 and p8 are membrane proteins, it is suggested that intercellular as well as intracellular movement of PVX involves a membrane-mediated process.

scholarly journals In Vivo Translation of the Triple Gene Block of Potato Virus X Requires Two Subgenomic mRNAs

1998 ◽  
Vol 72 (10) ◽  
pp. 8316-8320 ◽  
Author(s):  
Jeanmarie Verchot ◽  
Susan M. Angell ◽  
David C. Baulcombe
Keyword(s):  
Potato Virus ◽  
Triple Gene Block ◽  
Mrna Translation ◽  
Potato Virus X ◽  
Open Reading Frames ◽  
Movement Proteins ◽  
Gene Block ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

ABSTRACT The 25-kilodalton (25K), 12K, and 8K movement proteins of potato virus X are derived from overlapping open reading frames (ORFs). Using an in vivo complementation assay, we have shown that the 25K protein is expressed from a functionally monocistronic mRNA, whereas the 12K and 8K proteins are from a bicistronic mRNA. Translation of the 8K ORF is by leaky ribosome scanning through the 12K ORF.

scholarly journals Full length genome sequence of Polish isolate of Beet soil-borne virus confirms low level of genetic diversity.

2009 ◽  
Vol 56 (4) ◽  
Author(s):  
Natasza Borodynko ◽  
Beata Hasiów-Jaroszewska ◽  
Natalia Rymelska ◽  
Henryk Pospieszny
Keyword(s):  
Genetic Diversity ◽  
Genome Organization ◽  
Selective Pressure ◽  
Triple Gene Block ◽  
Synonymous Substitutions ◽  
Gene Block ◽  
Synonymous Mutations ◽  
High Level ◽  
Full Length Genome ◽  
First Time

The complete nucleotide sequence of a Polish isolate of Beet soil-borne virus was determined for the first time. The genome organization was identical with those previously established for isolates from Germany and China. A comparison of the Polish isolate with others deposited in GenBank revealed high level of nucleotide identity, about 98-100%, throughout the genome analyzed. The ratio between non-synonymous and synonymous substitutions was rather low suggesting a negative selective pressure. The non-synonymous mutations were particulary frequent in triple gene block.

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