scholarly journals Genome Organizations and Functional Analyses of a Novel Gammapartitivirus from Rhizoctonia solani AG-1 IA Strain D122

Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2254
Author(s):  
Meiling Zhang ◽  
Zhenrui He ◽  
Xiaotong Huang ◽  
Canwei Shu ◽  
Erxun Zhou
Keyword(s):  
Rhizoctonia Solani ◽  
Phylogenetic Analyses ◽  
Protoplast Regeneration ◽  
Sequence Alignments ◽  
Reading Frame ◽  
Transmission Electron ◽  
Viral Particles ◽  
The Family ◽  
20 Nm ◽  
Functional Analyses

Here, we describe a novel double-stranded (ds) RNA mycovirus designated Rhizoctonia solani dsRNA virus 5 (RsRV5) from strain D122 of Rhizoctonia solani AG-1 IA, the causal agent of rice sheath blight. The RsRV5 genome consists of two segments of dsRNA (dsRNA-1, 1894 bp and dsRNA-2, 1755 bp), each possessing a single open reading frame (ORF). Sequence alignments and phylogenetic analyses showed that RsRV5 is a new member of the genus Gammapartitivirus in the family Partitiviridae. Transmission electron microscope (TEM) images revealed that RsRV5 has isometric viral particles with a diameter of approximately 20 nm. The mycovirus RsRV5 was successfully removed from strain D122 by using the protoplast regeneration technique, thus resulting in derivative isogenic RsRV5-cured strain D122-P being obtained. RsRV5-cured strain D122-P possessed the traits of accelerated mycelial growth rate, increased sclerotia production and enhanced pathogenicity to rice leaves compared with wild type RsRV5-infection strain D122. Transcriptome analysis showed that three genes were differentially expressed between two isogenic strains, D122 and D122-P. These findings provided new insights into the molecular mechanism of the interaction between RsRV5 and its host, D122 of R. solani AG-1 IA.

scholarly journals A Novel Genus of Actinobacterial Tectiviridae

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1134 ◽  
Author(s):  
Steven M. Caruso ◽  
Tagide N. deCarvalho ◽  
Anthony Huynh ◽  
George Morcos ◽  
Nansen Kuo ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Dna Delivery ◽  
Transmission Electron ◽  
Viral Particles ◽  
Ancient Lineage ◽  
Linear Dsdna ◽  
Streptomyces Scabiei ◽  
Potato Crops

Streptomyces phages WheeHeim and Forthebois are two novel members of the Tectiviridae family. These phages were isolated on cultures of the plant pathogen Streptomyces scabiei, known for its worldwide economic impact on potato crops. Transmission electron microscopy showed viral particles with double-layered icosahedral capsids, and frequent instances of protruding nanotubes harboring a collar-like structure. Mass-spectrometry confirmed the presence of lipids in the virion, and serial purification of colonies from turbid plaques and immunity testing revealed that both phages are temperate. Streptomyces phages WheeHeim and Forthebois have linear dsDNA chromosomes (18,266 bp and 18,251 bp long, respectively) with the characteristic two-segment architecture of the Tectiviridae. Both genomes encode homologs of the canonical tectiviral proteins (major capsid protein, packaging ATPase and DNA polymerase), as well as PRD1-type virion-associated transglycosylase and membrane DNA delivery proteins. Comparative genomics and phylogenetic analyses firmly establish that these two phages, together with Rhodococcus phage Toil, form a new genus within the Tectiviridae, which we have tentatively named Deltatectivirus. The identification of a cohesive clade of Actinobacteria-infecting tectiviruses with conserved genome structure but with scant sequence similarity to members of other tectiviral genera confirms that the Tectiviridae are an ancient lineage infecting a broad range of bacterial hosts.

scholarly journals A tripartite ssDNA mycovirus from a plant pathogenic fungus is infectious as cloned DNA and purified virions

2020 ◽  
Vol 6 (14) ◽  
pp. eaay9634 ◽  
Author(s):  
Pengfei Li ◽  
Shuangchao Wang ◽  
Lihang Zhang ◽  
Dewen Qiu ◽  
Xueping Zhou ◽  
...  
Keyword(s):  
Fusarium Graminearum ◽  
Pathogenic Fungus ◽  
Phylogenetic Analyses ◽  
Colony Growth ◽  
Sequence Alignments ◽  
Dna Virus ◽  
Viral Dna ◽  
The Family ◽  
Circular Ssdna ◽  
Monopartite Genome

Here, we describe a tripartite circular single-stranded (ss) DNA mycovirus, named Fusarium graminearum gemytripvirus 1 (FgGMTV1). The genome of FgGMTV1 comprises three circular ssDNA segments (DNA-A, DNA-B, and DNA-C). Sequence alignments and phylogenetic analyses showed that FgGMTV1 is nested within the family Genomoviridae. We also constructed the first infectious DNA clones of a DNA mycovirus. Our results show that DNA-A and DNA-B are mutually interdependent for their replication and are associated with severely reduced colony growth and hypovirulence. DNA-C relies on DNA-A and DNA-B for replication and is necessary for the recovery of abnormal fungal phenotypes. DNA-C also enhances the accumulation of viral DNA in infected fungi and permits stable colonization and easy transmission via conidia. This is the first multipartite DNA virus isolated from a fungus. Our phylogenetic analyses also suggest that the multipartite genome of FgGMTV1 may have evolved from a monopartite genome of an ancient genomovirus.

scholarly journals Association of Rice Gall Dwarf Virus with Microtubules Is Necessary for Viral Release from Cultured Insect Vector Cells

2009 ◽  
Vol 83 (20) ◽  
pp. 10830-10835 ◽  
Author(s):  
Taiyun Wei ◽  
Tamaki Uehara-Ichiki ◽  
Naoyuki Miyazaki ◽  
Hiroyuki Hibino ◽  
Kenji Iwasaki ◽  
...  
Keyword(s):  
Insect Cells ◽  
Core Protein ◽  
Dwarf Virus ◽  
Insect Vector ◽  
Viral Transport ◽  
Transmission Electron ◽  
Viral Particles ◽  
The Family ◽  
Rice Gall Dwarf Virus ◽  
Vector Insect

ABSTRACT Vector insect cells infected with Rice gall dwarf virus, a member of the family Reoviridae, contained the virus-associated microtubules adjacent to the viroplasms, as revealed by transmission electron, electron tomographic, and confocal microscopy. The viroplasms, putative sites of viral replication, contained the nonstructural viral proteins Pns7 and Pns12, as well as core protein P5, of the virus. Microtubule-depolymerizing drugs suppressed the association of viral particles with microtubules and prevented the release of viruses from cells without significantly affecting viral multiplication. Thus, microtubules appear to mediate viral transport within and release of viruses from infected vector cells.

scholarly journals Evidence for a Novel Partitivirus Isolated From Entomopathogenic Nematode Steinernema Ceratophorum

2021 ◽  
Author(s):  
Shuangchao Wang ◽  
Irfan Ahmed ◽  
Xianhui Li ◽  
Lihua Guo
Keyword(s):  
Phylogenetic Analysis ◽  
Entomopathogenic Nematode ◽  
Plasmopara Viticola ◽  
Open Reading Frame ◽  
Sequence Alignments ◽  
Rna Dependent Rna Polymerase ◽  
Multiple Sequence ◽  
Reading Frame ◽  
Multiple Sequence Alignments ◽  
The Family

Abstract Nematodes are abundant, yet little is known about their viruses. In this study, we report a novel partitivirus isolated from Entomopathogenic nematode specie “Steinernema ceratophorum, named as Steinernema ceratophorum Partiti-like Virus 1 (ScPV1). The complete genome of ScPV1 is comprised of two dsRNA segments, dsRNA1 (2352 bp) and dsRNA2 (2196 bp) in length. Both dsRNAs contained a single open reading frame (ORF), encoding a putative RNA-dependent RNA polymerase (RdRp) and a coat protein (CP), respectively. The sequences of the RdRp and CP showed the highest similarity (47% and 33% identity, respectively) to Plasmopara viticola associated Partitivirus 7. Multiple sequence alignments and phylogenetic analysis of RdRp of ScPV1 with other selected viruses indicated that ScPV1 is the new member of genus Betapartitivirus in the family Partitiviridae.

scholarly journals Complete Nucleotide Sequence of a Partitivirus from Rhizoctonia solani AG-1 IA Strain C24

Viruses ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 703 ◽  
Author(s):  
Chen Liu ◽  
Miaolin Zeng ◽  
Meiling Zhang ◽  
Canwei Shu ◽  
Erxun Zhou
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Rhizoctonia Solani ◽  
Sheath Blight ◽  
Open Reading Frame ◽  
Rice Sheath Blight ◽  
Rna Dependent Rna Polymerase ◽  
Reading Frame ◽  
The Family

The complete genome of a novel double-stranded (ds) RNA mycovirus, named as Rhizoctonia solani partitivirus 5 (RsPV5), isolated from rice sheath blight fungus R. solani AG-1 IA strain C24, was sequenced and analysed. RsPV5 consists of two segments, dsRNA-1 (1899 nucleotides) and dsRNA-2 (1787 nucleotides). DsRNA-1 has an open reading frame (ORF) 1 that potentially codes for a protein of 584 amino acid (aa) containing the conserved motifs of a RNA-dependent RNA polymerase (RdRp), and dsRNA-2 also contains a ORF 2, encoding a putative capsid protein (CP) of 513 aa. Phylogenetic analysis revealed that RsPV5 clustered together with six other viruses in an independent clade of the genus Alphapartitivirus, indicating that RsPV5 was a new member of the genus Alphapartitivirus, within the family Partitiviridae.

Occurrence and distribution of Actinidia viruses in Shaanxi Province of China

Plant Disease ◽  
2020 ◽  
Author(s):  
Zhao Lei ◽  
Mengji Cao ◽  
Qianru Huang ◽  
Yicheng Wang ◽  
Jiaxiu Sun ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Virus Detection ◽  
International Committee ◽  
Shaanxi Province ◽  
Transmission Electron ◽  
Viral Particles ◽  
The Family ◽  
Novel Virus ◽  
Actinidia Spp ◽  
Yellowing Virus

Kiwifruit (Actinidia spp.) is an economically important fruit crop globally. China is the largest kiwifruit-growing country in the world, and Shaanxi Province is the major kiwifruit-growing region in China. A systematic survey detected various symptoms in kiwifruit plants grown in a commercial kiwifruit field in Shaanxi Province. Samples were collected from kiwifruit plants showing symptoms and used for virus detection by high-throughput sequencing. In addition to ten known kiwifruit viruses, three new viruses were detected and tentatively named Actinidia yellowing ringspot virus (AYRSpV), Actinidia yellowing virus 1 (AcYV1) and Actinidia yellowing virus 2 (AcYV2). The genome sequences of the three new viruses and four known viruses were determined. Based on the demarcation criteria of the International Committee on Taxonomy of Viruses (ICTV), AYRSpV might be a new member of the genus Ilarvirus in the family Bromoviridae, AcYV1 might be a new virus of the genus Waikavirus in the family Secoviridae, and AcYV2 might be a novel virus in the family Tombusviridae. Spherical viral particles were found in the samples infected with AYRSpV, AcYV1 and AcYV2 by transmission electron microscopy. Further analysis showed that all thirteen viruses can infect both A. deliciosa and A. chinensis, but the incidences of these infections vary among different kiwifruit cultivars in different regions. These results provide valuable information for understanding the viriome of kiwifruit in China.

scholarly journals Morphology, Ultrastructure, and Mitochondrial Genome of the Marine Non-Photosynthetic Bicosoecid Cafileria marina Gen. et sp. nov.

2019 ◽  
Vol 7 (8) ◽  
pp. 240
Author(s):  
Dagmar Jirsová ◽  
Zoltán Füssy ◽  
Jitka Richtová ◽  
Ansgar Gruber ◽  
Miroslav Oborník
Keyword(s):  
Mitochondrial Genome ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Ribosomal Gene ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Rock Surface ◽  
Transmission Electron ◽  
The Family

In this paper, we describe a novel bacteriophagous biflagellate, Cafileria marina with two smooth flagellae, isolated from material collected from a rock surface in the Kvernesfjorden (Norway). This flagellate was characterized by scanning and transmission electron microscopy, fluorescence, and light microscopy. The sequence of the small subunit ribosomal RNA gene (18S) was used as a molecular marker for determining the phylogenetic position of this organism. Apart from the nuclear ribosomal gene, the whole mitochondrial genome was sequenced, assembled, and annotated. Morphological observations show that the newly described flagellate shares key ultrastructural characters with representatives of the family Bicosoecida (Heterokonta). Intriguingly, mitochondria of C. marina frequently associate with its nucleus through an electron-dense disc at the boundary of the two compartments. The function of this association remains unclear. Phylogenetic analyses corroborate the morphological data and place C. marina with other sequence data of representatives from the family Bicosoecida. We describe C. marina as a new species from a new genus in this family.

scholarly journals Identification and Molecular Characterization of a Novel Partitivirus from Trichoderma atroviride NFCF394

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 578 ◽  
Author(s):  
Jeesun Chun ◽  
Han-Eul Yang ◽  
Dae-Hyuk Kim
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Molecular Characteristics ◽  
Trichoderma Atroviride ◽  
Double Stranded Rna ◽  
Reading Frame ◽  
Viral Particles ◽  
The Family ◽  
Isogenic Strains

An increasing number of novel mycoviruses have been described in fungi. Here, we report the molecular characteristics of a novel bisegmented double-stranded RNA (dsRNA) virus from the fungus Trichoderma atroviride NFCF394. We designated this mycovirus as Trichoderma atroviride partitivirus 1 (TaPV1). Electron micrographs of negatively stained, purified viral particles showed an isometric structure approximately of 30 nm in diameter. The larger segment (dsRNA1) of the TaPV1 genome comprised 2023 bp and contained a single open reading frame (ORF) encoding 614 amino acid (AA) residues of RNA-dependent RNA polymerase (RdRp). The smaller segment (dsRNA2) consisted of 2012 bp with a single ORF encoding 577 AA residues of capsid protein (CP). The phylogenetic analysis, based on deduced amino acid sequences of RdRp and CP, indicated that TaPV1 is a new member of the genus Alphapartitivirus in the family Partitiviridae. Virus-cured isogenic strains did not show significant changes in colony morphology. In addition, no changes in the enzymatic activities of β-1,3-glucanase and chitinase were observed in virus-cured strains. To the best of our knowledge, this is the first report of an Alphapartitivirus in T. atroviride.

scholarly journals Sequence analysis of a porcine enterovirus serotype 1 isolate: relationships with other picornaviruses

1999 ◽  
Vol 80 (8) ◽  
pp. 1929-1941 ◽  
Author(s):  
Michelle Doherty ◽  
Daniel Todd ◽  
Neil McFerran ◽  
Elizabeth M. Hoey
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Reading Frame ◽  
Sequence Identity ◽  
Porcine Enterovirus ◽  
Leader Protein ◽  
The Family ◽  
Serotype 1 ◽  
3D Sequences

The majority of the genomic sequence of a porcine enterovirus serotype 1 (PEV-1) isolate was determined. The genome was found to contain a large open reading frame which encoded a leader protein prior to the capsid protein region. This showed no sequence identity to other picornavirus leader regions and the sequence data suggested that it does not possess proteolytic activity. The 2A protease was small and showed considerable sequence identity to the aphthoviruses and to equine rhinovirus serotype 2. The 2A/2B junction possessed the typical cleavage site (NPG/P) exhibited by these viruses. The other proteins shared less than 40% sequence identity with equivalent proteins from other picornavirus genera. Phylogenetic analyses of the P1 and 3D sequences indicated that this virus forms a distinct branch of the family Picornaviridae. On the basis of results presented in this paper PEV-1 has been assigned to a new picornavirus genus. The phylogeny of the virus in relation to other picornaviruses is discussed.

A combined pseudoreplica-immunocytochemical technique for research and diagnostic virology

1990 ◽  
Vol 48 (3) ◽  
pp. 900-901
Author(s):  
Blayne Fritz ◽  
Stanley J. Naides ◽  
Kenneth Moore
Keyword(s):  
Phosphotungstic Acid ◽  
Immunogold Labelling ◽  
Uranyl Acetate ◽  
Distilled Water ◽  
Clinical Specimens ◽  
Tissue Sections ◽  
Specimen Retrieval ◽  
Transmission Electron ◽  
Viral Particles ◽  
Diagnostic Virology

The pseudoreplica method of staining viral particles for visualization by transmission electron microscopy is a very popular technique. The ability to concentrate clinical specimens while semi-embedding viral particles makes it especially well suited for morphologic and diagnostic virology. Immunolabelling viral particles with colloidal gold is a technique frequently employed by both research and diagnostic virologists. We have characterized a procedure which provides the advantage of both by modifying and combining pseudoreplica staining and immunogold labelling.Modification of specimen retrieval and delay of staining allows us to utilize pseudoreplica processed specimens within our standard immunogold labelling protocol. In brief, we absorbed samples onto 2% agarose, added.25% Formvar and wicked dry. We then floated the Formvar-virus film onto double distilled water, added grids and retrieved with parafilm. The Formvar-virus specimens were then treated as thin tissue sections within our standard two stage immunolabelling protocol. Following completion of immunogold labelling; each grid was negatively stained with phosphotungstic acid or uranyl acetate contrast stains.

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