scholarly journals Identification, Molecular Characterization, and Biology of a Novel Quadrivirus Infecting the Phytopathogenic Fungus Leptosphaeria biglobosa

Viruses ◽  
2018 ◽  
Vol 11 (1) ◽  
pp. 9 ◽  
Author(s):  
Unnati Shah ◽  
Ioly Kotta-Loizou ◽  
Bruce Fitt ◽  
Robert Coutts
Keyword(s):  
Phylogenetic Analysis ◽  
Pathogenic Fungus ◽  
Genome Structure ◽  
Amino Acid Sequences ◽  
Structural Proteins ◽  
Phytopathogenic Fungus ◽  
Molecular Characterisation ◽  
The Family ◽  
Dsrna Genome ◽  
Leptosphaeria Biglobosa

Here we report the molecular characterisation of a novel dsRNA virus isolated from the filamentous, plant pathogenic fungus Leptosphaeria biglobosa and known to cause significant alterations to fungal pigmentation and growth and to result in hypervirulence, as illustrated by comparisons between virus-infected and -cured isogenic fungal strains. The virus forms isometric particles approximately 40–45 nm in diameter and has a quadripartite dsRNA genome structure with size ranges of 4.9 to 4 kbp, each possessing a single ORF. Sequence analysis of the putative proteins encoded by dsRNAs 1–4, termed P1–P4, respectively, revealed modest similarities to the amino acid sequences of equivalent proteins predicted from the nucleotide sequences of known and suspected members of the family Quadriviridae and for that reason the virus was nominated Leptosphaeria biglobosa quadrivirus-1 (LbQV-1). Sequence and phylogenetic analysis using the P3 sequence, which encodes an RdRP, revealed that LbQV-1 was most closely related to known and suspected quadriviruses and monopartite totiviruses rather than other quadripartite mycoviruses including chrysoviruses and alternaviruses. Of the remaining encoded proteins, LbQV-1 P2 and P4 are structural proteins but the function of P1 is unknown. We propose that LbQV-1 is a novel member of the family Quadriviridae.

scholarly journals Isolation and Phylogenetic Analysis of Novel Viruses Infecting the Phytoplankton Phaeocystis globosa (Prymnesiophyceae)

2004 ◽  
Vol 70 (6) ◽  
pp. 3700-3705 ◽  
Author(s):  
C. P. D. Brussaard ◽  
S. M. Short ◽  
C. M. Frederickson ◽  
C. A. Suttle
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Polymerase ◽  
Coastal Waters ◽  
Common Ancestor ◽  
Genetic Relatedness ◽  
Amino Acid Sequences ◽  
Polymerase Gene ◽  
Phaeocystis Globosa ◽  
The Family ◽  
Algal Host

ABSTRACT Viruses infecting the harmful bloom-causing alga Phaeocystis globosa (Prymnesiophyceae) were readily isolated from Dutch coastal waters (southern North Sea) in 2000 and 2001. Our data show a large increase in the abundance of putative P. globosa viruses during blooms of P. globosa, suggesting that viruses are an important source of mortality for this alga. In order to examine genetic relatedness among viruses infecting P. globosa and other phytoplankton, DNA polymerase gene (pol) fragments were amplified and the inferred amino acid sequences were phylogenetically analyzed. The results demonstrated that viruses infecting P. globosa formed a closely related monophyletic group within the family Phycodnaviridae, with at least 96.9% similarity to each other. The sequences grouped most closely with others from viruses that infect the prymnesiophyte algae Chrysochromulina brevifilum and Chrysochromulina strobilus. Whether the P. globosa viruses belong to the genus Prymnesiovirus or form a separate group needs further study. Our data suggest that, like their phytoplankton hosts, the Chrysochromulina and Phaeocystis viruses share a common ancestor and that these prymnesioviruses and their algal host have coevolved.

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.

scholarly journals Taxonomic status of Bhanja and Kismayo viruses (family Bunyaviridae)

2012 ◽  
Vol 17 (4) ◽  
pp. 4-8
Author(s):  
A. S Klimentov ◽  
A. P Gmyl ◽  
A. M Butenko ◽  
L. V Gmyl ◽  
O. V Isaeva ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
The Family ◽  
L Segment

The nucleotide sequence of M= (1398 nucleotides and L= (6186 nucleotides) segments of the genome of Bhanja virus and L-segment (1297 nucleotides) of Kismayo virus has been partially determined. Phylogenetic analysis of deduced amino acid sequences showed that these viruses are novel members of the Flebovirus (Phlebovirus) genus in the family Bunyaviridae

scholarly journals A Novel Partitivirus in the Hypovirulent Isolate QT5-19 of the Plant Pathogenic Fungus Botrytis cinerea

Viruses ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 24 ◽  
Author(s):  
Md Kamaruzzaman ◽  
Guoyuan He ◽  
Mingde Wu ◽  
Jing Zhang ◽  
Long Yang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Botrytis Cinerea ◽  
Pathogenic Fungus ◽  
Amino Acid Sequences ◽  
Potato Dextrose Agar ◽  
Rna Dependent Rna Polymerase ◽  
Virus Particles ◽  
Genome Feature ◽  
Infected Tobacco ◽  
Hyphal Contact

A pink isolate (QT5-19) of Botrytis cinerea was compared with three gray isolates of B. cinerea for growth and morphogenesis on potato dextrose agar (PDA), and for pathogenicity on tobacco. A double-stranded (ds) RNA mycovirus infecting QT5-19 was identified based on its genome feature and morphology of the virus particles. The results showed that QT5-19 grew rapidly and established flourishing colonies as the gray isolates did. However, it is different from the gray isolates, as it failed to produce conidia and sclerotia asthe gray isolates did. QT5-19 hardly infected tobacco, whereas the gray isolates aggressively infected tobacco. Two dsRNAs were detected in QT5-19, dsRNA 1 and dsRNA 2, were deduced to encode two polypepetides with homology to viral RNA-dependent RNA polymerase (RdRp) and coat protein (CP), respectively. Phylogenetic analysis of the amino acid sequences of RdRp and CP indicated that the two dsRNAs represent the genome of a novel partitivirus in the genus Alphapartitivirus, designated here as Botrytis cinerea partitivirus 2 (BcPV2). BcPV2 in QT5-19 was successfully transmitted to the three gray isolates through hyphal contact. The resulting BcPV2-infected derivatives showed rapid growth on PDA with defects in conidiogenesis and sclerogenesis, and hypovirulence on tobacco. This study suggests that BcPV2 is closely associated with hypovirulence of B. cinerea.

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 .

Identification and Complete Genome Sequence of an Alternavirus From Airborne Spores of the Phytopathogenic Fungus Fusarium Bullatum

2021 ◽  
Author(s):  
Samira Mokhtari ◽  
Akhtar Ali
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Amino Acid Sequences ◽  
Phytopathogenic Fungus ◽  
Sequencing Analysis ◽  
Airborne Spores ◽  
Double Stranded Rna ◽  
Rapid Amplification ◽  
Dsrna Mycovirus ◽  
Blastn Search

Abstract A double-stranded RNA (dsRNA) mycovirus was isolated from airborne spores of Fusarium bullatum and was named Fusarium bullatum alternavirus 1 (FbAV1). Sequencing analysis and the rapid amplification of cDNA ends (RACE) of 5’ and 3’-end confirmed three segments: dsRNA1 (3546 nt), dsRNA2 (2511 nt) and dsRNA3 (2484 nt). BLASTN search of sequences showed that FbAV1 has 92-96% identity with Fusarium incarnatum Alternavirus 1 (FiAV1). Phylogenetic analysis of the RdRp amino acid sequences suggested that the dsRNA mycovirus in this study clustered with the newly proposed family “Alternaviridae”. This is the first report of FbAV1 mycovirus from airborne spores of a fungus F. bullatum.

scholarly journals Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot virus isolates

2019 ◽  
Vol 165 (1) ◽  
pp. 21-31 ◽  
Author(s):  
A. M. Dullemans ◽  
M. Botermans ◽  
M. J. D. de Kock ◽  
C. E. de Krom ◽  
T. A. J. van der Lee ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Complete Genome ◽  
New Genus ◽  
Sequence Data ◽  
Amino Acid Sequences ◽  
Ringspot Virus ◽  
Genome Sequences ◽  
The Family ◽  
Virus Isolates

Abstract To obtain insight into the sequence diversity of strawberry latent ringspot virus (SLRSV), isolates from collections and diagnostic samples were sequenced by high-throughput sequencing. For five SLRSV isolates, the complete genome sequences were determined, and for 18 other isolates nearly complete genome sequences were determined. The sequence data were analysed in relation to sequences of SLRSV and related virus isolates available in the NCBI GenBank database. The genome sequences were annotated, and sequences of the protease-polymerase (Pro-Pol) region and coat proteins (CPs) (large and small CP together) were used for phylogenetic analysis. The amino acid sequences of the Pro-Pol region were very similar, whereas the nucleotide sequences of this region were more variable. The amino acid sequences of the CPs were less similar, which was corroborated by the results of a serological comparison performed using antisera raised against different isolates of SLRSV. Based on these results, we propose that SLRSV and related unassigned viruses be assigned to a new genus within the family Secoviridae, named “Stralarivirus”. Based on the phylogenetic analysis, this genus should include at least three viruses, i.e., SLRSV-A, SLRSV-B and lychnis mottle virus. The newly generated sequence data provide a basis for designing molecular tests to screen for SLRSV.

scholarly journals Kolente virus, a rhabdovirus species isolated from ticks and bats in the Republic of Guinea

2013 ◽  
Vol 94 (12) ◽  
pp. 2609-2615 ◽  
Author(s):  
Elodie Ghedin ◽  
Matthew B. Rogers ◽  
Steven G. Widen ◽  
Hilda Guzman ◽  
Amelia P. A. Travassos da Rosa ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Complete Genome Sequence ◽  
Novel Species ◽  
Prototype Strain ◽  
Structural Proteins ◽  
Antigenic Relationship ◽  
Republic Of Guinea ◽  
The Family ◽  
Phylogenetic Resolution ◽  
The Republic

Kolente virus (KOLEV) is a rhabdovirus originally isolated from ticks and a bat in Guinea, West Africa, in 1985. Although tests at the time of isolation suggested that KOLEV is a novel rhabdovirus, it has remained largely uncharacterized. We assembled the complete genome sequence of the prototype strain DakAr K7292, which was found to encode the five canonical rhabdovirus structural proteins (N, P, M, G and L) with alternative ORFs (>180 nt) in the P and L genes. Serologically, KOLEV exhibited a weak antigenic relationship with Barur and Fukuoka viruses in the Kern Canyon group. Phylogenetic analysis revealed that KOLEV represents a distinct and divergent lineage that shows no clear relationship to any rhabdovirus except Oita virus, although with limited phylogenetic resolution. In summary, KOLEV represents a novel species in the family Rhabdoviridae.

scholarly journals Complete Genome Sequence of the First Chrysovirus From the Phytopathogenic Fungus Alternaria Solani on Potato in China

2021 ◽  
Author(s):  
Chenghui Hu ◽  
Siwei Li ◽  
Chunyan Wu ◽  
Yiran Mi ◽  
Qingnian Cai ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Alternaria Solani ◽  
Untranslated Regions ◽  
Phytopathogenic Fungus ◽  
Full Genome ◽  
Double Stranded Rna ◽  
The Family ◽  
Helminthosporium Victoriae ◽  
Dsrna Mycovirus ◽  
A New Species

Abstract The full genome of a double-stranded RNA (dsRNA) mycovirus, which was isolated from Alternaria solani strain DT-10 causing potato foliar disease and designated as Alternaria solani chrysovirus 1 (AsCV1), consisted of four dsRNA segments (dsRNA 1–4) with the length of 3600 bp, 3128 bp, 2996 bp, and 2714 bp, respectively. RNA-dependent RNA polymerase (RdRp, 1084 amino acids (aa)), putative capsid protein (905 aa), Alphachryso-P3 (835 aa), and Alphachryso-P4 (729 aa) were encoded by dsRNA1, dsRNA2, dsRNA3, and dsRNA4, respectively, which had the highest identities of 41.77%-72.38% to the counterparts of Helminthosporium victoriae virus 145S (HvV145S) in the genus Alphachrysovirus of the family Chrysoviridae. Moreover, the 5′-untranslated regions (UTRs) with several unique inserts (3–37 bp) and deletions (5–64 bp) of AsCV1 dsRNA 1–4 shared 51.65%-68.01% identities to those of HvV145S. Phylogenetic analysis of RdRp suggested that AsCV1 clustered the most closely with HvV145S. Based on the characteristics of distinct host, low identities of encoded proteins, special traits in 5′-UTRs of dsRNA 1–4, and phylogenetic analysis of RdRp, AsCV1 was confirmed to be a new species in the genus Alphachrysovirus. To our best knowledge, this is the first alphachrysovirus identified from phytopathogenic A. solani.

scholarly journals Date palm virus A: first plant virus found in date palm trees

2020 ◽  
Author(s):  
Ayoub Maachi ◽  
Tatsuya Nagata ◽  
João Marcos Fagundes Silva
Keyword(s):  
Phylogenetic Analysis ◽  
High Throughput Sequencing ◽  
Date Palm ◽  
Genomic Sequence ◽  
Triple Gene Block ◽  
Gene Organization ◽  
Amino Acid Sequences ◽  
Sequencing Data ◽  
Novel Genus ◽  
The Family

AbstractIn this work, a novel ssRNA (+) viral genomic sequence with gene organization typical of members of the subfamily Quinvirinae (family Betaflexiviridae) was identified using high throughput sequencing data of date palm obtained from the Sequence Read Archive database. The viral genome sequence consists of 7860 nucleotides and contains five ORFs encoding for the replication protein (Rep), triple gene block proteins 1, 2, 3 (TGB 1, 2 and 3) and coat protein (CP). Phylogenetic analysis based on the Rep and the CP amino acid sequences showed the closest relationship to garlic yellow mosaic-associated virus (GYMaV). Based on the demarcation criteria of the family Betaflexiviridae, this new virus, provisionally named date palm virus A (DPVA), could constitute a member of a novel genus. However, considering that DPVA and GYMaV share the same genomic organization and that they cluster together on the Rep phylogenetic analysis, they could also constitute a novel genus together, highlighting the necessity of a revision of the taxonomic criteria of the family Betaflexiviridae.

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