scholarly journals Complete genome sequence of a novel mitovirus isolated from Paris polyphylla var. yunnanensis

2021 ◽  
Author(s):  
Zeli Chen ◽  
Lu Chen ◽  
Rex Frimpong Anane ◽  
Zhe Wang ◽  
Like Gao ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Rna Virus ◽  
Genome Structure ◽  
Complementary Sequence ◽  
Reading Frame ◽  
A Genome ◽  
Paris Polyphylla ◽  
The Family

Abstract Paris mitovirus 1 (ParMV1) is a positive-sense RNA virus isolated from diseased Paris polyphylla var. yunnanensis plants in Wenshan, Yunnan. The complete genome sequence of ParMV1 consists of 2,751 nucleotides with a genome structure typical of the mitoviruses. ParMV1 genome has a single open reading frame (ORF: 358-2,637 nt) that encodes RNA-dependent RNA polymerase (RdRp) with a molecular mass of 86.42 kDa. ParMV1 contains six conserved motifs (Ι-VΙ) that are unique to mitoviruses. In addition, the 5′and 3′ terminals of the genome have a stable secondary structure, and the reverse complementary sequence forms a panhandle structure. Comparative genome analysis revealed that ParMV1 shares 23.1–40.6% amino acid (aa) and 32.3–45.7% nucleotide (nt) sequence identities with the RdRp of other mitoviruses. The phylogenetic tree inferred from RdRp aa sequence showed that ParMV1 clusters with mitoviruses, and hence should be considered as a new member of the genus Mitovirus in the family Motiviridae. This is the first report of a novel mitovirus infecting Paris polyphylla var. yunnanensis.

Characterization of a Novel Tombusviridae Species Isolated From Paris polyphylla var. yunnanensis

2021 ◽  
Author(s):  
Mingfu Zhao ◽  
Lu Chen ◽  
Rex Frimpong Anane ◽  
Zhe Wang ◽  
Zeli Chen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Sequence Alignments ◽  
Sequence Comparisons ◽  
Sequence Identity ◽  
Ssrna Virus ◽  
A Genome ◽  
Paris Polyphylla ◽  
The Family

Abstract A novel virus, Paris virus 2 (ParV2), was isolated from diseased Paris polyphylla var. yunnanensis, and its complete genome sequence was determined and analyzed. ParV2 is a positive-sense single-stranded RNA (+ssRNA) virus with a genome size of 4118 nucleotides. The ParV2 genome contains six putative open reading frames (ORFs) that encode proteins with predicted molecular weights of 40.14, 100.26, 7.31, 7.85, 26.09, and 8.77 kDa. The first ORF (ORF1) of ParV2 encodes a putative protein of 40.14 kDa (p40, nt: 20-1096), whiles the second ORF (ORF2, 888 aa) containing the GDD motif encodes the highly conserved RNA-dependent RNA polymerase protein (RdRP, nt:20-2683, p100, 100.26 kDa) of viruses in the family Tombusviridae. Multiple sequence alignments analysis showed that the complete genome sequence of ParV2 shares 31.7-55.5% nucleotide sequence identities with viruses in the family Tombusviridae. Ginger chlorotic fleck-associated tombusvirus (GCFaV-1,Accession No.QKE30557) had the highest sequence identity (55.5%) with ParV2, and also shares 59.2% RdRp and 34.9% CP amino acid sequence identity with GCFaV-1.Sequence comparisons and phylogenetic analysis of RdRp suggested that ParV2 is a novel member of the family Tombusviridae, and its closest known relative is GCFaV-1.

scholarly journals The Complete Genome Sequence of J Virus Reveals a Unique Genome Structure in the Family Paramyxoviridae

2005 ◽  
Vol 79 (16) ◽  
pp. 10690-10700 ◽  
Author(s):  
Philippa J. M. Jack ◽  
David B. Boyle ◽  
Bryan T. Eaton ◽  
Lin-Fa Wang
Keyword(s):  
Amino Acids ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Matrix Protein ◽  
Protein Gene ◽  
Genome Structure ◽  
Attachment Protein ◽  
A Genome ◽  
The Family

ABSTRACT J virus (J-V) was isolated from feral mice (Mus musculus) trapped in Queensland, Australia, during the early 1970s. Although studies undertaken at the time revealed that J-V was a new paramyxovirus, it remained unclassified beyond the family level. The complete genome sequence of J-V has now been determined, revealing a genome structure unique within the family Paramyxoviridae. At 18,954 nucleotides (nt), the J-V genome is the largest paramyxovirus genome sequenced to date, containing eight genes in the order 3′-N-P/V/C-M-F-SH-TM-G-L-5′. The two genes located between the fusion (F) and attachment (G) protein genes, which have been named the small hydrophobic (SH) protein gene and the transmembrane (TM) protein gene, encode putative proteins of 69 and 258 amino acids, respectively. The 4,401-nt J-V G gene, much larger than other paramyxovirus attachment protein genes sequenced to date, encodes a putative attachment protein of 709 amino acids and distally contains a second open reading frame (ORF) of 2,115 nt, referred to as ORF-X. Taken together, these novel features represent the most significant divergence to date from the common six-gene genome structure of Paramyxovirinae. Although genome analysis has confirmed that J-V can be classified as a member of the subfamily Paramyxovirinae, it cannot be assigned to any of the five existing genera within this subfamily. Interestingly, a recently isolated paramyxovirus appears to be closely related to J-V, and preliminary phylogenetic analyses based on putative matrix protein sequences indicate that these two viruses will likely represent a new genus within the subfamily Paramyxovirinae.

scholarly journals Complete genome sequence analysis of a novel bunyavirus isolated from Paris polyphylla var. yunnanensis

2021 ◽  
Author(s):  
Zeli Chen ◽  
Rex Frimpong Anane ◽  
Zhe Wang ◽  
Like Gao ◽  
Lu Chen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Rna Virus ◽  
Amino Acid Sequences ◽  
Reading Frame ◽  
Leaf Chlorosis ◽  
Paris Polyphylla ◽  
Complete Genome Sequence Analysis

Abstract A novel negative-stranded (ns) RNA virus tentatively named “Yunnan manyleaf paris rhizome negative-stranded virus 1” (YMPrNSV1), was isolated from a Paris polyphylla var. yunnanensis plant exhibiting leaf chlorosis and mosaic symptoms in Yunnan. Its complete genome sequence was determined using Illumina and Sanger sequencing. The genomes composed of three RNA segments (L, M and S) with each one containing a single open reading frame. Based on sequence identity and the presence of typical bunya-like domains/motifs, the proteins encoded by YMPrNSV1 were predicted to be: RNA-dependent RNA polymerase (RdRp), putative movement protein (MP), and nucleocapsid protein (NP). Sequence comparison analyses showed that the RdRp, MP and NP of YMPrNSV1 are highly similar to those of watermelon crinkle leaf-associated virus 2 (WCLaV-2), with 69.1%, 50.4% and 60.9% amino acid sequence identities respectively. Phylogenetic analysis based on deduced amino acid sequences of RdRp and NP suggested that YMPrNSV1 clustered with coguviruses in a clade, and that WCLaV-2 is the known closely related species to YMPrNSV1. Base on the above results, YMPrNSV1 should be regarded as a new member of genera Coguvirus, within the family Phenuiviridae.

scholarly journals Complete Genome Sequence of a Fusarium graminearum Double-Stranded RNA Virus in a Newly Proposed Family, Alternaviridae

2018 ◽  
Vol 6 (8) ◽  
Author(s):  
Hao He ◽  
Xiaoguang Chen ◽  
Pengfei Li ◽  
Dewen Qiu ◽  
Lihua Guo
Keyword(s):  
Phylogenetic Analysis ◽  
Fusarium Graminearum ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Rna Virus ◽  
Phytopathogenic Fungus ◽  
Double Stranded Rna ◽  
First Report ◽  
The Family

ABSTRACT We describe here a double-stranded RNA mycovirus, termed Fusarium graminearum alternavirus 1 (FgAV1/AH11), from the isolate AH11 of the phytopathogenic fungus F. graminearum . Phylogenetic analysis showed that FgAV1/AH11 belongs to a newly proposed family, Alternaviridae . This is the first report of a mycovirus in the family Alternaviridae that infects F. graminearum .

scholarly journals Complete genome sequence analysis of Seneca Valley virus-001, a novel oncolytic picornavirus

2008 ◽  
Vol 89 (5) ◽  
pp. 1265-1275 ◽  
Author(s):  
Laura M. Hales ◽  
Nick J. Knowles ◽  
P. Seshidar Reddy ◽  
Ling Xu ◽  
Carl Hay ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Rna Virus ◽  
Encephalomyocarditis Virus ◽  
Entry Site ◽  
Internal Ribosome Entry ◽  
Reading Frame ◽  
Encephalomyelitis Virus ◽  
Seneca Valley Virus

The complete genome sequence of Seneca Valley virus-001 (SVV-001), a small RNA virus, was determined and was shown to have typical picornavirus features. The 7280 nt long genome was predicted to contain a 5′ untranslated region (UTR) of 666 nt, followed by a single long open reading frame consisting of 6543 nt, which encodes a 2181 aa polyprotein. This polyprotein could potentially be cleaved into 12 polypeptides in the standard picornavirus L-4-3-4 layout. A 3′ UTR of 71 nt was followed by a poly(A) tail of unknown length. Comparisons with other picornaviruses showed that the P1, 2C, 3C and 3D polypeptides of SVV-001 were related most closely to those of the cardioviruses, although they were not related as closely to those of encephalomyocarditis virus and Theiler's murine encephalomyelitis virus as the latter were to each other. Most other regions of the polyprotein differed considerably from those of all other known picornaviruses. SVV-001 contains elements of an internal ribosome entry site reminiscent of that found in hepatitis C virus and a number of genetically diverse picornaviruses. SVV-001 is a novel picornavirus and it is proposed that it be classified as the prototype species in a novel genus named ‘Senecavirus’.

Complete genome sequence and evolution analysis of Eimeria stiedai RNA virus 1, a novel member of the family Totiviridae

2016 ◽  
Vol 161 (12) ◽  
pp. 3571-3576 ◽  
Author(s):  
Caiyan Xin ◽  
Bin Wu ◽  
Jianhua Li ◽  
Pengtao Gong ◽  
Ju Yang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Rna Virus ◽  
Evolution Analysis ◽  
The Family ◽  
Eimeria Stiedai

scholarly journals Complete Genome Sequence of a Novel Hypovirus from the Phytopathogenic Fungus Fusarium langsethiae

2017 ◽  
Vol 5 (9) ◽  
Author(s):  
Pengfei Li ◽  
Xiaoguang Chen ◽  
Hao He ◽  
Dewen Qiu ◽  
Lihua Guo
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Rna Virus ◽  
Phytopathogenic Fungus ◽  
First Report ◽  
The Family ◽  
Fusarium Langsethiae

ABSTRACT We describe a novel positive single-stranded RNA virus, termed Fusarium langsethiae hypovirus 1 (FlHV1), from the isolate AH32 of the phytopathogenic fungus Fusarium langsethiae. The properties of FlHV1 permit assignment to the genus Alphahypovirus in the family Hypoviridae. This is the first report of a mycovirus identified in F. langsethiae.

scholarly journals The First Complete Genome Sequence of a Novel Tetrastichus brontispae RNA Virus-1 (TbRV-1)

Viruses ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 257
Author(s):  
E Meng ◽  
Baozhen Tang ◽  
Francisco Sanchez-Garcia ◽  
Ting Qiao ◽  
Lang Fu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Amino Acid Sequence Identity ◽  
Rna Virus ◽  
Complete Sequence ◽  
Matrix Proteins ◽  
Sequence Identity ◽  
The Family ◽  
Family Rhabdoviridae

The complete sequence of a novel RNA virus isolated from Tetrastichus brontispae (TbRV-1) was determined to be 12,239 nucleotides in length with five non-overlapping, linearly arranged coding sequences (CDS), potentially encoding nucleoproteins, hypothetical proteins, matrix proteins, glycoproteins, and RNA-dependent RNA polymerases. Sequence analysis indicated that the RNA-dependent RNA polymerase of TbRV-1 shares a 65% nucleotide and 67% amino acid sequence identity with Hubei dimarhabdovirus 2, suggesting that TbRV-1 is a member of the dimarhabdovirus supergroup. This corresponded to the result of the phylogenetic analysis. The affiliation of TbRV-1 with members of the family Rhabdoviridae was further validated by similar transcription termination motifs (GGAACUUUUUUU) to the Drosophila sigmavirus. The prevalence of TbRV-1 in all tissues suggested that the virus was constitutive of, and not specific to, any wasp tissue. To our knowledge, this is the first report on the complete genome sequence of a dimarhabdovirus in parasitoids.

scholarly journals Complete Genome sequence of a new variant of jujube mosaic-associated virus isolated from jujube (Ziziphus jujuba Mill.) grown at Aksu in Xinjiang of China

2021 ◽  
Author(s):  
Jianyu Bai ◽  
Baojun Liu ◽  
Guoxin Zhang ◽  
Aixing Gu ◽  
Danbo Song ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Sequence Similarity ◽  
Genome Structure ◽  
Rnase H ◽  
Amino Acid Sequence Similarity ◽  
Coding Region ◽  
A Genome ◽  
New Variant

Abstract This work reports the discovery and the complete genome sequence of a novel member of the genus Badnavirus in the family Caulimoviridae from a Chinese jujube tree of known variety which grown in Aksu, Xinjiang, China. The symptoms of jujube leaves infected by the virus showed mosaic and malformation, and round chlorotic spots on infected fruits. The genome of this virus is a circular double-stranded DNA, which has the length of 7086 nt and has a genome structure similar to the one reported for jujube mosaic-associated virus (JuMaV), with five open reading frames (ORFs). High nucleotide and amino acid sequence similarity were seen between JuMaV and the new virus, and the nucleotide (NT) difference of the genome was greater than 20% in the RT/ Rnase H coding region of ORF3. Consequently, the virus was identified a new variant of JuMaV, and propose the name as jujube mosaic-associated virus A (JuMaVA).

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