scholarly journals Complete genome sequence of a novel fusarivirus from the phytopathogenic fungus Corynespora cassiicola

2021 ◽  
Author(s):  
Mingming Liu ◽  
Xintao Liu ◽  
Hui Zhao ◽  
Yunxia Ni ◽  
Min Jia ◽  
...  
Keyword(s):  
Chromosome Segregation ◽  
Open Reading Frames ◽  
Phytopathogenic Fungus ◽  
Corynespora Cassiicola ◽  
Rna Dependent Rna Polymerase ◽  
Rdrp Domain ◽  
Putative Protein ◽  
The Family ◽  
Reading Frames

Abstract Corynespora cassiicola is an important phytopathogenic fungus and it has severely impaired the production of crops. In this study, we report on the molecular characterization of a novel (+) ssRNA mycovirus, Corynespora cassiicola fusarivirus 1 (CcFV1) isolated from C. cassiicola strain 20200826-3-1. Excluding a poly (A) tail, the genome of the virus is 6491 nt containing three putative open reading frames. The large ORF1 encodes a polypeptide of 1524aa with a conserved RNA-dependent RNA polymerase (RdRp) domain, a helicase (Hel) domain, and a Phage-holin-3-6 (Phage-holin) domain. ORF2 encodes a polypeptide with a conserved Chromosome segregation ATPase (Smc) domain. The smallest ORF3 encodes a putative protein with an unknown function. Phylogenetic analysis based on the ORF1 and ORF2 of CcFV1 encoded polypeptide showed that CcFV1 is phylogenetically related to the newly proposed family Fusariviridae. Thus, we suggest that CcFV1 might be a novel member of the family Fusariviridae and is also the first discovered in C. cassiicola.

scholarly journals Molecular Characterization and Geographic Distribution of a Mymonavirus in the Population of Botrytis cinerea

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 432 ◽  
Author(s):  
Fangmin Hao ◽  
Mingde Wu ◽  
Guoqing Li
Keyword(s):  
Botrytis Cinerea ◽  
Sclerotinia Sclerotiorum ◽  
Cdna Sequence ◽  
Rna Virus ◽  
Open Reading Frames ◽  
Phytopathogenic Fungus ◽  
Rna Dependent Rna Polymerase ◽  
Rdrp Domain ◽  
The Family ◽  
Reading Frames

Here, we characterized a negative single-stranded (−ss)RNA mycovirus, Botrytis cinerea mymonavirus 1 (BcMyV1), isolated from the phytopathogenic fungus Botrytis cinerea. The genome of BcMyV1 is 7863 nt in length, possessing three open reading frames (ORF1–3). The ORF1 encodes a large polypeptide containing a conserved mononegaviral RNA-dependent RNA polymerase (RdRp) domain showing homology to the protein L of mymonaviruses, whereas the possible functions of the remaining two ORFs are still unknown. The internal cDNA sequence (10-7829) of BcMyV1 was 97.9% identical to the full-length cDNA sequence of Sclerotinia sclerotiorum negative stranded RNA virus 7 (SsNSRV7), a virus-like contig obtained from Sclerotinia sclerotiorum metatranscriptomes, indicating BcMyV1 should be a strain of SsNSRV7. Phylogenetic analysis based on RdRp domains showed that BcMyV1 was clustered with the viruses in the family Mymonaviridae, suggesting it is a member of Mymonaviridae. BcMyV1 may be widely distributed in regions where B. cinerea occurs in China and even over the world, although it infected only 0.8% of tested B. cinerea strains.

scholarly journals Molecular Characterization of A Novel Victorivirus Infecting Corynespora Cassiicola

2021 ◽  
Author(s):  
Mingming Liu ◽  
Yunxia Ni ◽  
Hui Zhao ◽  
Xintao Liu ◽  
Min Jia ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Corynespora Cassiicola ◽  
Rna Dependent Rna Polymerase ◽  
The Family ◽  
Fungal Viruses ◽  
Reading Frames

Abstract One victorivirus was detected in the isolate of Corynespora cassiicola strains 20180909-03, which was named Corynespora cassiicola victorivirus 1 (CcVV1). The whole-genome sequence of the virus was sequenced and identified. The CcVV1 genome is 5140 nt and contains 56.87%GC with two large open reading frames (ORFs) overlapping at the tetranucleotide AUGA. The two ORFs were predicted to encode coat protein (CP) and RNA-dependent RNA polymerase (RdRp) respectively, which were conservative in dsRNA fungal viruses of the family Totiviridae. Conservative domains comparison and phylogenetic analysis of the deduced amino acid sequence of RdRp and CP showed that CcVV1 was a new virus of the Victorivirus genus. As far as we know, it is the first report of a genomic sequence of the genus Victorivirus infecting Corynespora cassiicola.

scholarly journals Molecular Characterization of a Novel Virga-like Virus Isolated From Wheat

2021 ◽  
Author(s):  
Hua Li ◽  
Jun Guo ◽  
ZhongHua Zhao ◽  
Zhuangxin Ye ◽  
Jianping Chen ◽  
...  
Keyword(s):  
Rna Virus ◽  
Open Reading Frames ◽  
Polya Tail ◽  
Rna Dependent Rna Polymerase ◽  
Future Studies ◽  
Putative Protein ◽  
Host Growth ◽  
Positive Sense ◽  
Reading Frames

Abstract In this work, we report the isolation of a novel positive-sense single strand RNA virus from wheat, tentatively named Triticum aestivum-associated virga-like virus 1 (TaAVLV1). Further characterization revealed that the complete genome of TaAVLV1 was divided into two segments, RNA1 and RNA2, which were 3530 and 3466 nt long, excluding the polyA tail. These segments contained two open reading frames (ORFs). The ORF in RNA1 encoded an RNA-dependent RNA polymerase (RdRp), while the ORF in RNA2 encoded a putative protein carrying MET and HEL domains. Phylogenetic analysis based on the RdRp protein of each representative genus of Virgaviridae placed TaAVLV1 in the unclassified Virgaviridae clade of the Virgaviridae family. To our knowledge, this is the first report of virga-like virus isolated from wheat. Future studies will be conducted to examine its effect on host growth and development.

scholarly journals Molecular Characterization of Divergent Closterovirus Isolates Infecting Ribes Species

Viruses ◽  
2018 ◽  
Vol 10 (7) ◽  
pp. 369 ◽  
Author(s):  
Igor Koloniuk ◽  
Thanuja Thekke-Veetil ◽  
Jean-Sébastien Reynard ◽  
Irena Mavrič Pleško ◽  
Jaroslava Přibylová ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Protein ◽  
Heat Shock Protein 90 ◽  
Open Reading Frames ◽  
Coat Proteins ◽  
Rna Dependent Rna Polymerase ◽  
The Family ◽  
Host Cell Wall ◽  
Reading Frames

Five isolates of a new member of the family Closteroviridae, tentatively named blackcurrant leafroll-associated virus 1 (BcLRaV-1), were identified in the currant. The 17-kb-long genome codes for 10 putative proteins. The replication-associated polyprotein has several functional domains, including papain-like proteases, methyltransferase, Zemlya, helicase, and RNA-dependent RNA polymerase. Additional open reading frames code for a small protein predicted to integrate into the host cell wall, a heat-shock protein 70 homolog, a heat-shock protein 90 homolog, two coat proteins, and three proteins of unknown functions. Phylogenetic analysis showed that BcLRaV-1 is related to members of the genus Closterovirus, whereas recombination analysis provided evidence of intraspecies recombination.

Molecular characterization of a novel mycovirus isolated from Rhizoctonia solani AG-1 IA 9-11

2021 ◽  
Author(s):  
Yang Sun ◽  
Yan qiong Li ◽  
Wen han Dong ◽  
Ai li Sun ◽  
Ning wei Chen ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Rna Virus ◽  
Dsrna Virus ◽  
Open Reading Frames ◽  
The Family ◽  
Significant Amino Acid Sequence ◽  
Overlapping Open Reading Frames ◽  
Significant Amino Acid ◽  
Reading Frames

Abstract The complete genome of the dsRNA virus isolated from Rhizoctonia solani AG-1 IA 9–11 (designated as Rhizoctonia solani dsRNA virus 11, RsRV11 ) were determined. The RsRV11 genome was 9,555 bp in length, contained three conserved domains, SMC, PRK and RT-like super family, and encoded two non-overlapping open reading frames (ORFs). ORF1 potentially coded for a 204.12 kDa predicted protein, which shared low but significant amino acid sequence identities with the putative protein encoded by Rhizoctonia solani RNA virus HN008 (RsRV-HN008) ORF1. ORF2 potentially coded for a 132.41 kDa protein which contained the conserved motifs of the RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis indicated that RsRV11 was clustered with RsRV-HN008 in a separate clade independent of other virus families. It implies that RsRV11, along with RsRV-HN008 possibly a new fungal virus taxa closed to the family Megabirnaviridae, and RsRV11 is a new member of mycoviruses.

scholarly journals Characterization and Genomic Analysis of Phage asccφ28, a Phage of the Family Podoviridae Infecting Lactococcus lactis

2008 ◽  
Vol 74 (11) ◽  
pp. 3453-3460 ◽  
Author(s):  
Steven E. Kotsonis ◽  
Ian B. Powell ◽  
Christopher J. Pillidge ◽  
Gaëtan K. Y. Limsowtin ◽  
Alan J. Hillier ◽  
...  
Keyword(s):  
Lactococcus Lactis ◽  
Dna Hybridization ◽  
Burst Size ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Full Genome Sequence ◽  
The Family ◽  
Reading Frames ◽  
Dairy Fermentation

ABSTRACT Bacteriophage asccφ28 infects dairy fermentation strains of Lactococcus lactis. This report describes characterization of asccφ28 and its full genome sequence. Phage asccφ28 has a prolate head, whiskers, and a short tail (C2 morphotype). This morphology and DNA hybridization to L. lactis phage P369 DNA showed that asccφ28 belongs to the P034 phage species, a group rarely encountered in the dairy industry. The burst size of asccφ28 was found to be 121 ± 18 PFU per infected bacterial cell after a latent period of 44 min. The linear genome (18,762 bp) contains 28 possible open reading frames (ORFs) comprising 90% of the total genome. The ORFs are arranged bidirectionally in recognizable functional modules. The genome contains 577 bp inverted terminal repeats (ITRs) and putatively eight promoters and four terminators. The presence of ITRs, a phage-encoded DNA polymerase, and a terminal protein that binds to the DNA, along with BLAST and morphology data, show that asccφ28 more closely resembles streptococcal phage Cp-1 and the φ29-like phages that infect Bacillus subtilis than it resembles common lactococcal phages. The sequence of this phage is the first published sequence of a P034 species phage genome.

scholarly journals Molecular Characterization of a Novel Fusarivirus Infecting the Plant-pathogenic Fungus Alternaria Solani

2021 ◽  
Author(s):  
Jie Wei Gong ◽  
Hong Liu ◽  
Fei Xiao Zhu ◽  
Yun Shi Zhao ◽  
Le Jia Cheng ◽  
...  
Keyword(s):  
Amino Acids ◽  
Pathogenic Fungus ◽  
Alternaria Solani ◽  
Open Reading Frames ◽  
Phytopathogenic Fungus ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Putative Protein

Abstract A novel mycovirus belonging to the proposed family "Fusariviridae" was discovered in Alternaria Solani by sequencing a double-stranded RNA extracted from this phytopathogenic fungus. The virus was tentatively named “Alternaria solani fusarivirus 1” (AsFV1). AsFV1 has a single-stranded positive-sense (+ssRNA) genome of 6,845 nucleotides containing three open reading frames (ORFs) and a poly(A) tail. The largest ORF, ORF1 encodes a large polypeptide of 1,556 amino acids (aa) with conserved RNA-dependent RNA polymerase and helicase domains. The ORF2 and ORF3 have overlapping regions, encoding a putative protein of 522 amino acids (aa) and a putative protein of 105 amino acids (aa) respectively, for which function is unknown now. Multiple sequence alignments and phylogenetic analysis revealed AsFV1 belonging to Fusariviridae. This is the first report of the full-length nucleotide sequence of a fusarivirus infected with Alternaria solani.

scholarly journals Genomic characterization of three novel Pseudomonas phages within the subfamily of Autographivirinae isolated from organic waste

2020 ◽  
Author(s):  
Jacob B Jørgensen ◽  
Amaru M Djuurhus ◽  
Alexander B. Carstens ◽  
Witold Kot ◽  
Cindy E. Morris ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Organic Waste ◽  
New Genus ◽  
Open Reading Frames ◽  
Genomic Comparison ◽  
Double Stranded Dna ◽  
The Family ◽  
Genomic Characterization ◽  
Reading Frames

AbstractThree phages targeting Pseudomonas syringae GAW0113 have been isolated from organic waste samples: Pseudomonas phage Bertil, Misse and Strit. The phages have double-stranded DNA genomes ranging from 41342 to 41374 bp in size comprising 50 to 51 open reading frames. The three phages genomes are highly similar and genomic comparison analyses shows that they all belong to the Autographivirinae subfamily of the family Podoviridae. The phages are however only distantly related to other members of this family, and have limited gene synteny with type-phages of other genera within Autographivirinae, suggesting that the newly isolated phages could represent a new genus.

scholarly journals A Gene Encoding l-Methionine γ-Lyase Is Present in Enterobacteriaceae Family Genomes: Identification and Characterization of Citrobacter freundiil-Methionine γ-Lyase

2005 ◽  
Vol 187 (11) ◽  
pp. 3889-3893 ◽  
Author(s):  
Ilya V. Manukhov ◽  
Daria V. Mamaeva ◽  
Sergei M. Rastorguev ◽  
Nicolai G. Faleev ◽  
Elena A. Morozova ◽  
...  
Keyword(s):  
Shigella Flexneri ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
High Sequence Identity ◽  
E Coli ◽  
The Family ◽  
Serovar Typhimurium ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT Citrobacter freundii cells produce l-methionine γ-lyase when grown on a medium containing l-methionine. The nucleotide sequence of the hybrid plasmid with a C. freundii EcoRI insert of about 3.0 kbp contained two open reading frames, consisting of 1,194 nucleotides and 1,296 nucleotides, respectively. The first one (denoted megL) encoded l-methionine γ-lyase. The enzyme was overexpressed in Escherichia coli and purified. The second frame encoded a protein belonging to the family of permeases. Regions of high sequence identity with the 3′-terminal part of the C. freundii megL gene located in the same regions of Salmonella enterica serovar Typhimurium, Shigella flexneri, E. coli, and Citrobacter rodentium genomes were found.

Molecular Characterization of a Novel Partitivirus and a Fusarivirus Co-infected in the Nigrospora Sphaerica Fungus

2021 ◽  
Author(s):  
Jie Zhong ◽  
Ze Zhong Yang ◽  
Xin Yang ◽  
Zhao Jiang Guo ◽  
Wen Xie ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Pathogenic Fungus ◽  
Rna Replication ◽  
Open Reading Frames ◽  
Helicase Domain ◽  
Polya Tail ◽  
Viral Rdrp ◽  
The Family ◽  
Reading Frames

Abstract Here we reported the molecular characterization of two novel mycoviruses co-infected in a plant pathogenic fungus, Nigrospora sphaerica that were designated as Nigrospora sphaerica fusarivirus 1 (NsFV1) and Nigrospora sphaerica partitivirus 1 (NsPV1), respectively. NsFV1 has an undivided genome of 6,147 bp, excluding the polyA tail, and was predicted to contain two nonoverlapping open reading frames (ORF1 and 2). The larger ORF1 encoded a polyprotein containing a conserved RNA-dependent RNA polymerase (RdRp) and a helicase domain that have functions for RNA replication, and the smaller ORF2 encoded a putative protein with an unknown function. The NsPV1 was consists of two genome segments, which were in lengths of 1,796 bp and 1,455 bp, respectively. Each of the two dsRNAs had a single ORF and were deduced to encode proteins with homology to viral RdRp and coat protein (CP), respectively, in the family Partitiviridae. Phylogenetic analysis showed that NsFV1 was placed within the newly proposed family Fusariviridae, while NsPV1 was belonging to the genus Gammapartitivirus in the family Partitiviridae. This was the first description of mycovirses infected the fungus N. sphaerica.

Sign in / Sign up

Export Citation Format

Share Document