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 Molecular Characterization of a Novel Ourmia-Like Virus Infecting Phoma matteucciicola

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 231 ◽  
Author(s):  
Jia Zhou ◽  
Yuhua Wang ◽  
Xiaofei Liang ◽  
Changping Xie ◽  
Wenbo Liu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Rna Polymerase ◽  
Molecular Characterization ◽  
Open Reading Frame ◽  
Single Open Reading Frame ◽  
Rna Dependent Rna Polymerase ◽  
Reading Frame ◽  
The Family

Here, we report a novel (+) ssRNA mycovirus, Phoma matteucciicola ourmia-like virus 1 (PmOLV1), isolated from Phoma matteucciicola strain LG915-1. The genome of PmOLV1 was 2603 nucleotides long and contained a single open reading frame (ORF), which could be translated into a product of RNA-dependent RNA polymerase (RdRp) by both standard and mitochondrial genetic codons. Cellular fractionation assay indicated that PmOLV1 RNAs are likely more enriched in mitochondria than in cytoplasm. Phylogenetic analysis indicated that PmOLV1 is a new member of the genus Penoulivirus (recently proposed) within the family Botourmiaviridae.

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.

scholarly journals Complete nucleotide sequence of a novle botourmiavirus from the rice blast fungus, Magnaporthe oryzae isolate SH05

2021 ◽  
Author(s):  
Qingchao Deng ◽  
Xuan Zhou ◽  
Simnin Shuai ◽  
Hong Zheng ◽  
Hang Ding ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Rice Blast ◽  
Rice Blast Fungus ◽  
Plasmopara Viticola ◽  
Open Reading Frame ◽  
Genome Comparison ◽  
Rna Dependent Rna Polymerase ◽  
Reading Frame ◽  
Blast Fungus ◽  
The Family

Abstract A novel mycovirus, proposed name Magnaporthe oryzae botourmiavirus 9 (MoBV9), was described in the rice blast fungus, Magnaporthe oryzae isolate SH05. The virus has a positive single-stranded (+) ss RNA genome of 2,812 nucleotides and contains a single open reading frame predicted to encode an RNA-dependent RNA polymerase closely related to some unclassified viruses of the family Botourmiaviridae, such as Plasmopara viticola lesion associated ourmia-like virus 44, Plasmopara viticola lesion associated ourmia-like virus 47and Cladosporium uredinicola ourmiavirus 1. Genome comparison and phylogenetic analysis supported the notion that MoBV9 is a new member of the family Botourmiaviridae.

scholarly journals phastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP

2018 ◽  
Author(s):  
Ritika Ramani ◽  
Katie Krumholz ◽  
Yifei Huang ◽  
Adam Siepel
Keyword(s):  
Phylogenetic Analysis ◽  
Software Package ◽  
Evolutionary Conservation ◽  
Web Interface ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Tree Models ◽  
Key Features ◽  
The Web

ABSTRACTThe Phylogenetic Analysis with Space/Time models (PHAST) package is a widely used software package for comparative genomics that has been freely available for download since 2002. Here we introduce a web interface (phastWeb) that makes it possible to use two of the most popular programs in PHAST, phastCons and phyloP, without downloading and installing the PHAST software. This interface allows users to upload a sequence alignment and either upload a corresponding phylogeny or have one estimated from the alignment. After processing, users can visualize alignments and conservation scores as genome browser tracks, and download estimated tree models and raw scores for further analysis. Altogether, this resource makes key features of the PHAST package conveniently available to a broad audience.AVAILABILITYphastWeb is freely available on the web at http://compgen.cshl.edu/phastweb/. The website provides instructions as well as [email protected]

scholarly journals PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP

2018 ◽  
Vol 35 (13) ◽  
pp. 2320-2322 ◽  
Author(s):  
Ritika Ramani ◽  
Katie Krumholz ◽  
Yi-Fei Huang ◽  
Adam Siepel
Keyword(s):  
Phylogenetic Analysis ◽  
Software Package ◽  
Evolutionary Conservation ◽  
Web Interface ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Tree Models ◽  
Key Features ◽  
The Web

Abstract Summary The Phylogenetic Analysis with Space/Time models (PHAST) package is a widely used software package for comparative genomics that has been freely available for download since 2002. Here, we introduce a web interface (phastWeb) that makes it possible to use two of the most popular programs in PHAST, phastCons and phyloP, without downloading and installing the PHAST software. This interface allows users to upload a sequence alignment and either upload a corresponding phylogeny or have one estimated from the alignment. After processing, users can visualize alignments and conservation scores as genome browser tracks and download estimated tree models and raw scores for further analysis. Altogether, this resource makes key features of the PHAST package conveniently available to a broad audience. Availability and implementation PhastWeb is freely available on the web at http://compgen.cshl.edu/phastweb/. The website provides instructions as well as examples.

Sequencing and Phylogenetic analysis of vlhA gene from Mycoplasma synoviae field isolates associated with Eggshell apex abnormality

2018 ◽  
Author(s):  
P. Sumitha ◽  
K. Sukumar ◽  
S. Srivignesh
Keyword(s):  
Phylogenetic Analysis ◽  
Tamil Nadu ◽  
Reference Strain ◽  
Molecular Detection ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Mycoplasma Synoviae ◽  
Multiple Sequence Alignments ◽  
Layer Chicken ◽  
Clustal Omega

Eggshell apex abnormality (EAA) associated with Mycoplasma synoviae is occurring regularly in many commercial layer chicken farms of Tamil Nadu. Choanal cleft swabs were collected from EAA affected poultry farms, subjected for isolation and molecular detection of M. synoviae. Among 16 farms investigated M. synoviae could be isolated in six farms. All the farms were positive for M. synoviae in PCR. Among six isolates three isolates (VCandRI-NKL-SV3, VCandRI-NKL- PV6, VCandRI-NKL-KV2) from severe clinical outbreak were sequenced for vlhA gene and compared with the available sequences from the Gene Bank (NCBI) using multiple sequence alignments software - Clustal Omega and Bio edit programs. Analysis showed that the VCandRI,NKL-SV3 and VCandRI-NKL-KV2 were more similar (94.3%) to each other. Point mutation percentage of isolates VCandRI-NKL-PV6, VCandRI-NKL-SV3 and VCandRI-NKL-KV2 isolates in comparison with reference strain KC506806 were 12, 5.1 and 1.8% respectively. The phylogenetic analysis indicated that the VCandRI-NKL-SV3 and VCandRI-NKL-PV6 were closely evolved with VCandRI-NKL-KV2. VCandRI-NKL-KV2 was closely related to sequence of Mycoplasma synoviae from Brazil.

scholarly journals Phylogenetic analysis of Heliothis armigera cytoplasmic polyhedrosis virus type 14 and a series of dwarf segments found in the genome

2007 ◽  
Vol 88 (3) ◽  
pp. 991-997 ◽  
Author(s):  
Yanqiu Li ◽  
Jiamin Zhang ◽  
Yang Li ◽  
Li Tan ◽  
Wuguo Chen ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Virus Type ◽  
Major Capsid Protein ◽  
Heliothis Armigera ◽  
Insect Virus ◽  
Rna Dependent Rna Polymerase ◽  
Cytoplasmic Polyhedrosis Virus ◽  
Reading Frame ◽  
The Family ◽  
Polyhedrosis Virus

Full-length nucleotide sequences for the genome segments (S1–S6) of Heliothis armigera cytoplasmic polyhedrosis virus type 14 (HaCPV-14) have been characterized. Each segment consists of a single open reading frame with conserved motifs AGAA and AGCU at the 5′ and 3′ ends, respectively. Comparison of the proteins of HaCPV-14 with those of other members of the family Reoviridae suggests that S1 encodes an RNA-dependent RNA polymerase (RdRp), whilst S2 encodes a major capsid protein of the virus. Phylogenetic analysis of RdRps from 16 viruses in the family Reoviridae reveals that the genera Cypovirus and Oryzavirus may have originated from a common insect virus ancestor. A series of viable dwarf segments originating from S5 of HaCPV-14 has been identified. Analysis of the predicted secondary structures for these dwarf segments suggests that the signals essential for replication and packaging are located within the terminal sequences of these segments.

scholarly journals Positive natural selection in primate genes of the type I interferon response

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Elena N. Judd ◽  
Alison R. Gilchrist ◽  
Nicholas R. Meyerson ◽  
Sara L. Sawyer
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Type I Interferon ◽  
Interferon Response ◽  
Type I ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Interferon Stimulated Genes ◽  
Interferon Induction

Abstract Background The Type I interferon response is an important first-line defense against viruses. In turn, viruses antagonize (i.e., degrade, mis-localize, etc.) many proteins in interferon pathways. Thus, hosts and viruses are locked in an evolutionary arms race for dominance of the Type I interferon pathway. As a result, many genes in interferon pathways have experienced positive natural selection in favor of new allelic forms that can better recognize viruses or escape viral antagonists. Here, we performed a holistic analysis of selective pressures acting on genes in the Type I interferon family. We initially hypothesized that the genes responsible for inducing the production of interferon would be antagonized more heavily by viruses than genes that are turned on as a result of interferon. Our logic was that viruses would have greater effect if they worked upstream of the production of interferon molecules because, once interferon is produced, hundreds of interferon-stimulated proteins would activate and the virus would need to counteract them one-by-one. Results We curated multiple sequence alignments of primate orthologs for 131 genes active in interferon production and signaling (herein, “induction” genes), 100 interferon-stimulated genes, and 100 randomly chosen genes. We analyzed each multiple sequence alignment for the signatures of recurrent positive selection. Counter to our hypothesis, we found the interferon-stimulated genes, and not interferon induction genes, are evolving significantly more rapidly than a random set of genes. Interferon induction genes evolve in a way that is indistinguishable from a matched set of random genes (22% and 18% of genes bear signatures of positive selection, respectively). In contrast, interferon-stimulated genes evolve differently, with 33% of genes evolving under positive selection and containing a significantly higher fraction of codons that have experienced selection for recurrent replacement of the encoded amino acid. Conclusion Viruses may antagonize individual products of the interferon response more often than trying to neutralize the system altogether.

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