scholarly journals Complete Genome Sequence of a Novel Potyvirus Infecting Miscanthus Sinensis (Silver Grass)

2021 ◽  
Author(s):  
Zacharie Leblanc ◽  
Marie-Emilie Gauthier ◽  
Ruvini Lelwala ◽  
Candace Elliott ◽  
Cassie McMaster ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Genome Sequence ◽  
Maize Dwarf Mosaic Virus ◽  
Miscanthus Sinensis ◽  
Sequence Motifs ◽  
Conserved Sequence ◽  
Ssrna Virus ◽  
The Family ◽  
Post Entry ◽  
Full Length Genome

Abstract Here, we describe the full-length genome sequence of a novel potyvirus, tentatively named “miscanthus sinensis mosaic virus” (MsiMV), isolated from Miscanthus sinensis (silver grass) held in a post entry quarantine facility following its initial import into Western Australia, Australia. The MsiMV genome encompasses 9604 nucleotides (nt) encoding a 3071 amino acids (aa) polyprotein with conserved sequence motifs. The MsiMV genome is most closely related to sorghum mosaic virus (SrMV) with 74% nt and 78.5% aa sequence identity to the SrMV polyprotein region. Phylogenetic analysis based on the polyprotein grouped MsiMV with SrMV, sugarcane mosaic virus (SCMV) and maize dwarf mosaic virus (MDMV). This is the first report of a novel monopartite ssRNA virus in Miscanthus sinensis related to members of the genus Potyvirus in the family Potyviridae.

Complete Genome Sequence of a Novel Ourmia-like Mycovirus Infecting the Phytopathogenic Fungus Botryosphaeria Dothidea

2021 ◽  
Author(s):  
Liying Sun ◽  
Ziqian Lian ◽  
Subha Das ◽  
Jingxian Luo ◽  
Ida Bagus Andika
Keyword(s):  
Amino Acid ◽  
Genome Sequence ◽  
Amino Acid Sequences ◽  
Shanxi Province ◽  
Phytopathogenic Fungus ◽  
Botryosphaeria Dothidea ◽  
Reading Frame ◽  
Ring Rot ◽  
Ssrna Virus ◽  
The Family

Abstract In this study, we describe the full-length genome sequence of a novel ourmia-like mycovirus, tentatively designated Botryosphaeria dothidea ourmia-like virus 1 (BdOLV1), isolated from the phytopathogenic fungus, Botryosphaeria dothidea strain P8, associated with apple ring rot in Shanxi province, China. The complete BdOLV1 genome is comprised of 2797 nucleotides, a positive-sense (+) single-stranded RNA (ssRNA) with a single open reading frame (ORF). The ORF putatively encodes a 642-amino acid polypeptide with conserved RNA-dependent RNA polymerase (RdRp) motifs, related to viruses of the family Botourmiaviridae. Phylogenetic analysis based on the RdRp amino acid sequences showed that BdOLV1 is grouped with oomycete-infecting unclassified viruses closely related to the genus Botoulivirus in Botourmiaviridae. This is the first report of a novel (+)ssRNA virus in B. dothidea related to the genus Botoulivirus in the family Botourmiaviridae.

Full-length genome sequence of the tospovirus melon severe mosaic virus

2017 ◽  
Vol 162 (5) ◽  
pp. 1419-1422 ◽  
Author(s):  
M. Ciuffo ◽  
L. Nerva ◽  
M. Turina
Keyword(s):  
Mosaic Virus ◽  
Genome Sequence ◽  
Full Length ◽  
Full Length Genome

scholarly journals Complete Genome Sequence of Vallota Mosaic Virus Detected In A Narcissus Bulb Imported From The United States to Japan

2021 ◽  
Author(s):  
Yuya Imamura ◽  
Moritsugu Oishi ◽  
Yuji Fujiwara ◽  
Hironobu Yanagisawa
Keyword(s):  
United States ◽  
Mosaic Virus ◽  
Genome Sequence ◽  
Distinct Species ◽  
First Record ◽  
The United States ◽  
Viral Agent ◽  
Coat Protein Region ◽  
Post Entry ◽  
Rapid Amplification

Abstract Narcissus (Narcissus albidus) imported from the United States exhibited leaf chlorosis during post-entry quarantine. We employed next-generation sequencing (NGS) on symptomatic leaf samples and detected vallota mosaic virus (ValMV) belonging to the genus Potyvirus, family Potyviridae, as the viral agent. Sanger sequencing of PCR and rapid amplification of cDNA ends based on NGS contigs revealed that ValMV was 9,451 nucleotides (nt) in length, excluding the poly(A) tail. Nucleotide and amino acid (aa) sequences of the coat protein region had over 98% identity to previously reported ValMV isolates. At each of the 10 mature protein regions, however, sequence identity with other potyviruses was 49.5–71.9% nt and 18.3–78.9% aa, values that are below the species demarcation criteria for Potyviridae. Phylogenetic analysis revealed that our ValMV isolate is most closely related to known ValMV and is grouped within other potyviruses. Taken together, our results indicate that the newly isolated ValMV belongs to a distinct species of Potyvirus. This study provides the first report of the complete ValMV genome sequence and the first record of this virus from the narcissus.

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 Mdm1 Locus and Maize Resistance to Maize dwarf mosaic virus

Plant Disease ◽  
2007 ◽  
Vol 91 (2) ◽  
pp. 185-190 ◽  
Author(s):  
M. W. Jones ◽  
M. G. Redinbaugh ◽  
R. Louie
Keyword(s):  
Mosaic Virus ◽  
Fragment Length Polymorphism ◽  
Bulked Segregant Analysis ◽  
Inbred Lines ◽  
Maize Dwarf Mosaic Virus ◽  
Resistant Parent ◽  
Resistant Lines ◽  
The Family ◽  
Maize Resistance ◽  
Symptom Type

Previously, Mdm1, a gene controlling resistance to Maize dwarf mosaic virus (MDMV), was identified in the inbred line Pa405. The gene was tightly linked to the restriction fragment length polymorphism marker umc85 on the short arm of chromosome 6. This chromosomal region is also the location of resistance genes to two other viruses in the family Potyviridae, Sugarcane mosaic virus (SCMV) and Wheat streak mosaic virus (WSMV). A diverse collection of 115 maize inbred lines was evaluated for resistance to MDMV and SCMV, and for MDMV resistance loci on chromosome 6S. Forty-six resistant inbred lines were crossed to three MDMVsusceptible inbred lines to develop F2 populations. The F2 populations were inoculated with MDMV and scored for infection and symptom type. Environmental factors influenced both the rate and type of symptom development. Bulked segregant analysis of each F2 population indicated that, in 42 of 43 MDMV-resistant lines, chromosome 6S markers found in the resistant parent also were present in the bulked resistant but not the susceptible tissue. Markers previously associated with resistance to both SCMV and WSMV on chromosome 3 and to WSMV on chromosome 10 were associated with resistance in nine and seven of the F2 populations, respectively. These data suggest that Mdm1 or closely linked genes on chromosome 6S are associated with MDMV resistance in most germplasm, but that other loci also may affect resistance.

scholarly journals Genome organization of the densovirus from Bombyx mori (BmDNV-1) and enzyme activity of its capsid

2001 ◽  
Vol 82 (11) ◽  
pp. 2821-2825 ◽  
Author(s):  
Y. Li ◽  
Z. Zádori ◽  
H. Bando ◽  
R. Dubuc ◽  
G. Fédière ◽  
...  
Keyword(s):  
Amino Acids ◽  
Enzyme Activity ◽  
Bombyx Mori ◽  
Genome Sequence ◽  
Genome Organization ◽  
Phospholipase A ◽  
Sequence Motifs ◽  
Unique Region ◽  
Conserved Sequence

Bombyx mori densovirus (BmDNV-1), on the basis of the previously reported genome sequence, constitutes by itself a separate genus (Iteravirus) within the Densovirinae subfamily of parvoviruses. Inconsistencies in the genome organization, however, necessitated its reassessment. The genome sequence of new clones was determined and resulted in a completely different genome organization. The corrected sequence also contained conserved sequence motifs found in other parvoviruses. Some amino acids in the highly conserved domain in the unique region of VP1 were shared by critical amino acids in the catalytic site and Ca2+-binding loop of secreted phospholipase A2, such as from snake and bee venoms. Expression of this domain and determination of enzyme activity demonstrated that capsids have a phospholipase A2 activity thus far unknown to occur in viruses. This viral phospholipase A2, which is required shortly after entry into the cell, showed a substrate preference for phosphatidylethanolamine and phosphatidylcholine over phosphatidylinositol.

scholarly journals DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

2021 ◽  
Author(s):  
Yanrong Ji ◽  
Zhihan Zhou ◽  
Han Liu ◽  
Ramana V Davuluri
Keyword(s):  
Dna Sequences ◽  
Regulatory Elements ◽  
Ease Of Use ◽  
Fine Tuning ◽  
Supplementary Information ◽  
Sequence Motifs ◽  
Semantic Relationship ◽  
Accurate Identification ◽  
Conserved Sequence ◽  
Genome Wide

Abstract Motivation Deciphering the language of non-coding DNA is one of the fundamental problems in genome research. Gene regulatory code is highly complex due to the existence of polysemy and distant semantic relationship, which previous informatics methods often fail to capture especially in data-scarce scenarios. Results To address this challenge, we developed a novel pre-trained bidirectional encoder representation, named DNABERT, to capture global and transferrable understanding of genomic DNA sequences based on up and downstream nucleotide contexts. We compared DNABERT to the most widely used programs for genome-wide regulatory elements prediction and demonstrate its ease of use, accuracy and efficiency. We show that the single pre-trained transformers model can simultaneously achieve state-of-the-art performance on prediction of promoters, splice sites and transcription factor binding sites, after easy fine-tuning using small task-specific labeled data. Further, DNABERT enables direct visualization of nucleotide-level importance and semantic relationship within input sequences for better interpretability and accurate identification of conserved sequence motifs and functional genetic variant candidates. Finally, we demonstrate that pre-trained DNABERT with human genome can even be readily applied to other organisms with exceptional performance. We anticipate that the pre-trained DNABERT model can be fined tuned to many other sequence analyses tasks. Availability and implementation The source code, pretrained and finetuned model for DNABERT are available at GitHub (https://github.com/jerryji1993/DNABERT). Supplementary information Supplementary data are available at Bioinformatics online.

Complete genome sequence of a recombinant isolate of yambean mosaic virus from Canavalia ensiformis

Virus Genes ◽  
2021 ◽  
Author(s):  
Renan de Souza Cascardo ◽  
Lorenna L. Pires ◽  
Lorhan L. Leal ◽  
F. Murilo Zerbini ◽  
Poliane Alfenas-Zerbini ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Canavalia Ensiformis
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