scholarly journals POPULATION GENETICS ANALYSIS OF Garlic virus A, Garlic virus B, Garlic virus C AND Garlic virus X

2019 ◽  
Vol 18 (3) ◽  
Author(s):  
Maria Bereda ◽  
Elżbieta Paduch-Cichal
Keyword(s):  
Population Size ◽  
Negative Selection ◽  
Balancing Selection ◽  
Amino Acid Sequences ◽  
Virus Species ◽  
Nucleic Acid Binding ◽  
The Family ◽  
Virus C ◽  
Garlic Virus ◽  
Pressure Analysis

Garlic virus A (GarV-A), Garlic virus B (GarV-B), Garlic virus C (GarV-C) and Garlic virus X (GarV-X) are members of the genus Allexivirus in the family Alphaflexiviridae. In this study, we collected 10, 30, 10 and 14 isolates of GarV-A, GarV-B, GarV-C and GarV-X, respectively, from different parts of Poland. All sequences of coat protein (CP) and nucleic-acid binding protein (NABP) regions of Allexivirus isolates available in GenBank were also included in this study. The nucleotide and amino acid sequences identities within each population differed substantially depending on the region of the genome and virus species. The results of selection pressure analysis showed that populations of each Allexivirus underwent negative selection, but the extent of the negative selection varied. It was also concluded that the GarV-A and GarV-C populations underwent a decrease in population size or balancing selection, while the GarV-B and GarV-X populations underwent an increase in population size. It was concluded that both populations of GarV-X evolved independently in each respective area, in contrast to populations of GarV-A, GarV-B and GarV-C.

scholarly journals Molecular characterization of the coat protein gene revealed considerable diversity of viral species complex in Garlic (Allium sativum L.)

2020 ◽  
Author(s):  
Abel Debebe Mitiku ◽  
Dawit Tesfaye Degefu ◽  
Adane Abraham ◽  
Desta Mejan ◽  
Pauline Asami ◽  
...  
Keyword(s):  
Amino Acid ◽  
Coat Protein ◽  
Species Complex ◽  
Sequence Data ◽  
Amino Acid Sequences ◽  
Viral Gene ◽  
Planting Material ◽  
Virus C ◽  
Garlic Virus ◽  
Material Exchange

AbstractGarlic is one of the most crucial Allium vegetables used as seasoning of foods. It has a lot of benefits from the medicinal and nutritional point of view; however, its production is highly constrained by both biotic and abiotic challenges. Among these, viral infections are the most prevalent factors affecting crop productivity around the globe. This experiment was conducted on eleven selected garlic accessions and three improved varieties collected from different garlic growing agro-climatic regions of Ethiopia. This study aimed to identify and characterize the isolated garlic virus using the coat protein (CP) gene and further determine their phylogenetic relatedness. RNA was extracted from fresh young leaves, thirteen days old seedlings, which showed yellowing, mosaic, and stunting symptoms. Pairwise molecular diversity for CP nucleotide and amino acid sequences were calculated using MEGA5. Maximum Likelihood tree of CP nucleotide sequence data of Allexivirus and Potyvirus were conducted using PhyML, while a neighbor-joining tree was constructed for the amino acid sequence data using MEGA5. From the result, five garlic viruses were identified viz. Garlic virus C (78.6 %), Garlic virus D (64.3 %), Garlic virus X (78.6 %), Onion yellow dwarf virus (OYDV) (100%), and Leek yellow stripe virus (LYSV) (78.6 %). The study revealed the presence of complex mixtures of viruses with 42.9 % of the samples had co-infected with a species complex of Garlic virus C, Garlic virus D, Garlic virus X, OYDV, and LYSV. Pairwise comparisons of the isolated Potyviruses and Allexiviruses species revealed high identity with that of the known members of their respected species. As an exception, less within species identity was observed among Garlic virus C isolates as compared with that of the known members of the species. Finally, our results highlighted the need for stepping up a working framework to establish virus-free garlic planting material exchange in the country which could result in the reduction of viral gene flow across the country.Author SummaryGarlic viruses are the most devastating disease since garlic is the most vulnerable crop due to their vegetative nature of propagation. Currently, the garlic viruses are the aforementioned production constraint in Ethiopia. However, so far very little is known on the identification, diversity, and dissemination of garlic infecting viruses in the country. Here we explore the prevalence, genetic diversity, and the presence of mixed infection of garlic viruses in Ethiopia using next generation sequencing platform. Analysis of nucleotide and amino acid sequences of coat protein genes from infected samples revealed the association of three species from Allexivirus and two species from Potyvirus in a complex mixture. Ultimately the article concludes there is high time to set up a working framework to establish garlic free planting material exchange platform which could result in a reduction of viral gene flow across the country.

scholarly journals Consensus proposals for classification of the family Hepeviridae

2014 ◽  
Vol 95 (10) ◽  
pp. 2223-2232 ◽  
Author(s):  
Donald B. Smith ◽  
Peter Simmonds ◽  
Shahid Jameel ◽  
Suzanne U. Emerson ◽  
Tim J. Harrison ◽  
...  
Keyword(s):  
Mammalian Species ◽  
Cutthroat Trout ◽  
Hepatitis E ◽  
Amino Acid Sequences ◽  
Sequence Information ◽  
Virus Species ◽  
Wide Range ◽  
The Family ◽  
Novel Variants

The family Hepeviridae consists of positive-stranded RNA viruses that infect a wide range of mammalian species, as well as chickens and trout. A subset of these viruses infects humans and can cause a self-limiting acute hepatitis that may become chronic in immunosuppressed individuals. Current published descriptions of the taxonomical divisions within the family Hepeviridae are contradictory in relation to the assignment of species and genotypes. Through analysis of existing sequence information, we propose a taxonomic scheme in which the family is divided into the genera Orthohepevirus (all mammalian and avian hepatitis E virus (HEV) isolates) and Piscihepevirus (cutthroat trout virus). Species within the genus Orthohepevirus are designated Orthohepevirus A (isolates from human, pig, wild boar, deer, mongoose, rabbit and camel), Orthohepevirus B (isolates from chicken), Orthohepevirus C (isolates from rat, greater bandicoot, Asian musk shrew, ferret and mink) and Orthohepevirus D (isolates from bat). Proposals are also made for the designation of genotypes within the human and rat HEVs. This hierarchical system is congruent with hepevirus phylogeny, and the three classification levels (genus, species and genotype) are consistent with, and reflect discontinuities in the ranges of pairwise distances between amino acid sequences. Adoption of this system would include the avoidance of host names in taxonomic identifiers and provide a logical framework for the assignment of novel variants.

scholarly journals Discovery of a Novel Member of the Carlavirus Genus from Soybean (Glycine max L. Merr.)

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 223
Author(s):  
Thanuja Thekke-Veetil ◽  
Nancy K. McCoppin ◽  
Houston A. Hobbs ◽  
Glen L. Hartman ◽  
Kris N. Lambert ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Triple Gene Block ◽  
Red Clover ◽  
Amino Acid Sequences ◽  
Predicted Amino Acid Sequence ◽  
Nucleic Acid Binding ◽  
Gene Block ◽  
The Family ◽  
Sequence Identities

A novel member of the Carlavirus genus, provisionally named soybean carlavirus 1 (SCV1), was discovered by RNA-seq analysis of randomly collected soybean leaves in Illinois, USA. The SCV1 genome contains six open reading frames that encode a viral replicase, triple gene block proteins, a coat protein (CP) and a nucleic acid binding protein. The proteins showed highest amino acid sequence identities with the corresponding proteins of red clover carlavirus A (RCCVA). The predicted amino acid sequence of the SCV1 replicase was only 60.6% identical with the replicase of RCCVA, which is below the demarcation criteria for a new species in the family Betaflexiviridae. The predicted replicase and CP amino acid sequences of four SCV1 isolates grouped phylogenetically with those of members of the Carlavirus genus in the family Betaflexiviridae. The features of the encoded proteins, low nucleotide and amino acid sequence identities of the replicase with the closest member, and the phylogenetic grouping suggest SCV1 is a new member of the Carlavirus genus.

scholarly journals Garlic viral complex: identification of Potyviruses and Carlavirus in Central Brazil

2001 ◽  
Vol 26 (3) ◽  
pp. 619-626 ◽  
Author(s):  
THOR V. M. FAJARDO ◽  
MARTA NISHIJIMA ◽  
JOSÉ A. BUSO ◽  
ANTÔNIO C. TORRES ◽  
ANTÔNIO C. ÁVILA ◽  
...  
Keyword(s):  
Coat Protein ◽  
Blot Hybridization ◽  
Amino Acid Sequences ◽  
Onion Yellow Dwarf Virus ◽  
Nucleotide Sequence Analysis ◽  
Virus Species ◽  
Dot Blot ◽  
Geographical Regions ◽  
Yellow Dwarf Virus ◽  
Garlic Virus

Garlic viruses often occur in complex infections in nature. In this study, a garlic virus complex, collected in fields in Brazil, was purified. RT-PCR was performed using specific primers designed from the consensus regions of the coat protein genes of Onion yellow dwarf virus, a garlic strain (OYDV-G) and Leek yellow stripe virus (LYSV). cDNA of Garlic common latent virus (GCLV) was synthesized using oligo-dT and random primers. By these procedures individual garlic virus genomes were isolated and sequenced. The nucleotide sequence analysis associated with serological data reveals the presence of two Potyvirus OYDV-G and LYSV, and GCLV, a Carlavirus, simultaneously infecting garlic plants. Deduced amino acid sequences of the Brazilian isolates were compared with related viruses reported in different geographical regions of the world. The analysis showed closed relations considering the Brazilian isolates of OYDV-G and GCLV, and large divergence considering LYSV isolate. The detection of these virus species was confirmed by specific reactions observed when coat protein genes of the Brazilian isolates were used as probes in dot-blot and Southern blot hybridization assays. In field natural viral re-infection of virus-free garlic was evaluated.

scholarly journals A new virus found in garlic virus complex is a member of possible novel genus of the family Betaflexiviridae (order Tymovirales)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6285 ◽  
Author(s):  
Leonardo A. Da Silva ◽  
Athos S. Oliveira ◽  
Fernando L. Melo ◽  
Daniel M.P. Ardisson-Araújo ◽  
Francisco V. Resende ◽  
...  
Keyword(s):  
Vegetative Propagation ◽  
High Frequency ◽  
High Throughput Sequencing ◽  
Protein Gene ◽  
Germplasm Collection ◽  
Replicase Gene ◽  
Virus Species ◽  
The Family ◽  
Virus Complex ◽  
Garlic Virus

Plant vegetative propagation strategies for agricultural crops cause the accumulation of viruses, resulting in the formation of virus complexes or communities. The cultivation of garlic is based on vegetative propagation and more than 13 virus species from the genera Potyvirus, Allexivirus and Carlavirus have been reported. Aiming for an unbiased identification of viruses from a garlic germplasm collection in Brazil, total RNA from eight garlic cultivars was sequenced by high-throughput sequencing (HTS) technology. Although most viruses found in this study were previously reported, one of them did not belong to any known genera. This putative new virus was found in seven out of eight garlic cultivars and phylogenetic data positioned it as representative of an independent evolutionary lineage within family Betaflexiviridae. This virus has been tentatively named garlic yellow mosaic-associated virus (GYMaV), sharing highest nucleotide identities with African oil palm ringspot virus (genus Robigovirus) and potato virus T (genus Tepovirus) for the replicase gene, and with viruses classified within genus Foveavirus for the coat protein gene. Due to its high frequency in garlic cultivars, GYMaV should be considered in upcoming surveys of pathogens in this crop and in the development of virus-free garlic plants.

scholarly journals Detection of three Allexivirus species infecting garlic in Brazil

2004 ◽  
Vol 39 (8) ◽  
pp. 735-740 ◽  
Author(s):  
Péricles de Albuquerque Melo Filho ◽  
Tatsuya Nagata ◽  
André Nepomuceno Dusi ◽  
José Amauri Buso ◽  
Antonio Carlos Torres ◽  
...  
Keyword(s):  
Chenopodium Quinoa ◽  
Polyclonal Antiserum ◽  
Virus Species ◽  
Rt Pcr ◽  
The One ◽  
Dot Elisa ◽  
Virus C ◽  
Serological Data ◽  
Virus Genomes ◽  
Garlic Virus

Garlic viruses often occur in mixed infections under field conditions. In this study, garlic samples collected in three geographical areas of Brazil were tested by Dot-ELISA for the detection of allexiviruses using monoclonal specific antibodies to detect Garlic virus A (GarV-A), Garlic virus B (GarV-B), Garlic virus C (GarV-C) and a polyclonal antiserum able to detect the three virus species mentioned plus Garlic virus D (GarV-D). The detected viruses were biologically isolated by successive passages through Chenopodium quinoa. Reverse Transcriptase Polimerase Chain Reaction (RT-PCR) was performed using primers designed from specific regions of the coat protein genes of Japanese allexiviruses available in the Genetic Bank of National Center of Biotechnology Information (NCBI). By these procedures, individual garlic virus genomes were isolated and sequenced. The nucleotide and amino acid sequence analysis and the one with serological data revealed the presence of three distinct allexiviruses GarV-C, GarV-D and a recently described allexivirus, named Garlic mite-borne filamentous virus (GarMbFV), in Brazil.

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 Salinadaptatus halalkaliphilus gen. nov., sp. nov., a haloalkaliphilic archaeon isolated from salt pond in Inner Mongolia Autonomous Region, China

2020 ◽  
Author(s):  
Qiong Xue ◽  
Zhenqiang Zuo ◽  
Heng Zhou ◽  
Jian Zhou ◽  
Shengjie Zhang ◽  
...  
Keyword(s):  
Inner Mongolia ◽  
Type Strain ◽  
Amino Acid Sequences ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Autonomous Region ◽  
Salt Pond ◽  
A Genome ◽  
The Family ◽  
Inner Mongolia Autonomous Region

A haloalkaliphilic strain XQ-INN 246T was isolated from the sediment of a salt pond in Inner Mongolia Autonomous Region, China. Cells of the strain were rods, motile and strictly aerobic. The strain was able to grow in the presence of 2.6–5.3 M NaCl (optimum concentration is 4.4 M) at 30–50 °C (optimum temperature is 42 °C) and pH 7.0–10.0 (optimum pH is 8.0–8.5). The whole genome sequencing of strain XQ-INN 246T revealed a genome size of 4.52 Mbp and a DNA G+C content of 62.06 mol%. Phylogenetic tree based on 16S rRNA gene sequences and concatenated amino acid sequences of 122 single-copy conserved proteins revealed a robust lineage of the strain XQ-INN 246T with members of related genera of the family Natrialbaceae . The strain possessed the polar lipids of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. No glycolipids were detected. Based on phylogenetic analysis, phenotypic characteristics, chemotaxonomic properties and genome relatedness, the isolate was proposed as the type strain of a novel species of a new genus within the family Natrialbaceae, for which the name Salinadaptatus halalkaliphilus gen. nov., sp. nov. is proposed. The type strain is XQ-INN 246T (=CGMCC 1.16692T=JCM 33751T).

Sign in / Sign up

Export Citation Format

Share Document