Transmission of Garlic virus B, Garlic virus C, Garlic virus D and Garlic virus X by Aceria tulipae (Keifer) in leek

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.

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Effect of Two Allexivirus Isolates on Garlic Yield

Plant Disease ◽

10.1094/pd-90-0898 ◽

2006 ◽

Vol 90 (7) ◽

pp. 898-904 ◽

Cited By ~ 14

Author(s):

E. E. Cafrune ◽

M. C. Perotto ◽

V. C. Conci

Keyword(s):

Allium Sativum ◽

Negative Control ◽

Yield Losses ◽

Assay Condition ◽

First Report ◽

Virus Complex ◽

Significant Yield ◽

Virus C ◽

Garlic Virus ◽

Assay Conditions

Garlic (Allium sativum) is infected by numerous viruses forming a viral-complex, which is widely distributed in the garlic production regions of Argentina. This work is the first report of the effect of two Allexivirus isolates, Garlic virus A (GarV-A) and Garlic virus C (GarV-C), on garlic yield. Garlic cvs. Morado-INTA and Blanco-IFFIVE were used in the experiments, and four treatments were evaluated: plants inoculated with GarV-A only, GarV-C only, virus-free plants (negative control), and plants infected with the virus-complex. Assays were performed in anti-aphid cages and in the field during 2002 and 2003. GarV-A caused significant reductions in bulb weight (14 to 32%) and diameter (6 to 11%) compared with the negative control in the two cultivars under both assay conditions. GarV-C caused less damage than GarV-A (15% in weight and 5% in diameter) with respect to the negative control in cv. Blanco-IFFIVE, and did not produce significant yield losses in cv. Morado-INTA in either year or under either assay condition.

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

Acta Scientiarum Polonorum Hortorum Cultus ◽

10.24326/asphc.2019.3.10 ◽

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.

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Detecção de allexivírus em primórdios foliares de alho via RT-PCR

Summa Phytopathologica ◽

10.1590/s0100-54052008000300014 ◽

2008 ◽

Vol 34 (3) ◽

pp. 267-269

Author(s):

Robson José do Nascimento ◽

Gilvan Pio-Ribeiro ◽

Roseane Cavalcanti dos Santos ◽

Péricles de Albuquerque Melo Filho

Keyword(s):

Southern Blot ◽

Rio Grande ◽

Rio Grande Do Sul ◽

Rt Pcr ◽

Virus C ◽

Garlic Virus

Nos procedimentos de detecção de allexivirus em bulbos de alho, tem-se como rotina o plantio de bulbilhos para obtenção de tecido foliar a ser analisado via testes sorológicos e/ou moleculares. A disponibilização das plantas em casa de vegetação implica em gastos com a manutenção e requer, em média, 30 dias. Em áreas isentas desses vírus, corre-se, ainda, o risco de sua introdução e disseminação. No presente trabalho buscou-se ajustar um protocolo para detecção rápida de allexivírus em alho a partir de primórdios foliares. Bulbilhos de alho para consumo, oriundos do Rio Grande do Sul e importados da Argentina foram dissecados para obtenção de primórdios foliares e extração de RNA total a partir de 0,1 g de tecido. A seguir foram conduzidas reações de RT-PCR com um par de oligonucleotídeos, capaz de gerar um fragmento de aproximadamente 500 pb relativo à porção interna do gene da capa protéica de várias espécies do gênero Allexivirus. Uma banda com tamanho aproximado de 500 pb foi visualizada, em gel de agarose e, posteriormente, confirmada por Southern Blot e por seqüenciamento como sendo Garlic vírus C (GarV-C, AY170322.1). A obtenção de RNA total diretamente de primórdios foliares de bulbilhos e seu uso em análise de RT-PCR, constituem-se em uma metodologia econômica, rápida e segura para a detecção de allexivírus em bulbos de alho.

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Recombinant expression of Garlic virus C (GARV-C) capsid protein in insect cells and its potential for the production of specific antibodies

Microbiological Research ◽

10.1016/j.micres.2006.06.016 ◽

2008 ◽

Vol 163 (3) ◽

pp. 354-361 ◽

Cited By ~ 5

Author(s):

Miguel Alves-Júnior ◽

Fernanda Menezes Marraccini ◽

Péricles de Albuquerque Melo Filho ◽

André Nepomuceno Dusi ◽

Gilvan Pio-Ribeiro ◽

...

Keyword(s):

Capsid Protein ◽

Insect Cells ◽

Recombinant Expression ◽

Specific Antibodies ◽

Virus C ◽

Garlic Virus

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Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes

International Journal of Molecular Sciences ◽

10.3390/ijms22136791 ◽

2021 ◽

Vol 22 (13) ◽

pp. 6791

Author(s):

Yeonhwa Jo ◽

Chang-Gi Back ◽

Kook-Hyung Kim ◽

Hyosub Chu ◽

Jeong Hun Lee ◽

...

Keyword(s):

Rna Sequencing ◽

In Silico Analysis ◽

Sequencing Data ◽

Yield And Quality ◽

Bulbous Plant ◽

Virus C ◽

Dominant Bacteria ◽

Garlic Virus ◽

Silico Analysis

Garlic (Allium sativum) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues using garlic RNA-sequencing data. The number of identified microbial species was the highest in inflorescences, followed by flowers and bulb cloves. With the Kraken2 tool, 57% of identified microbial reads were assigned to bacteria and 41% were assigned to viruses. Fungi only made up 1% of microbial reads. At the species level, Streptomyces lividans was the most dominant bacteria while Fusarium pseudograminearum was the most abundant fungi. Several allexiviruses were identified. Of them, the most abundant virus was garlic virus C followed by shallot virus X. We obtained a total of 14 viral genome sequences for four allexiviruses. As we expected, the microbial community varied depending on the tissue types, although there was a dominant microorganism in each tissue. In addition, we found that Kraken2 was a very powerful and efficient tool for the bacteria using RNA-sequencing data with some limitations for virome study.

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Detection of three Allexivirus species infecting garlic in Brazil

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2004000800002 ◽

2004 ◽

Vol 39 (8) ◽

pp. 735-740 ◽

Cited By ~ 15

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.

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First report of garlic viruses A, B and C on garlic (Allium sativum L.) in Tunisia

Plant Disease ◽

10.1094/pdis-08-21-1706-pdn ◽

2021 ◽

Author(s):

Chadha Ayed ◽

Imen Hamdi ◽

Asma Najar ◽

Armelle Marais ◽

Chantal Faure ◽

...

Keyword(s):

Synergistic Effects ◽

Direct Sequencing ◽

Germplasm Collection ◽

Rt Pcr ◽

Serological Tests ◽

First Report ◽

Three Samples ◽

Pcr Assays ◽

Virus C ◽

Garlic Virus

Mite-borne viruses belonging to the genus Allexivirus (family Alphaflexiviridae) commonly occur on garlic in many parts of the world. There are usually asymptomatic and cause small damage to the plants, but often occur in mixed infection with potyviruses and carlaviruses, with synergistic effects reducing crop quality and leading to higher losses (Taglienti et al. 2017). Their occurrence on Tunisian garlic crops was studied here in the same garlic germplasm collection mentioned in a previous first report (Ayed et al. 2019). Leaf samples from a total of 66 garlic accessions were tested by DAS-ELISA using specific antibodies (DSMZ, Germany) against garlic virus A (GarV-A), garlic virus B (GarV-B) and garlic virus C (GarV-C). These serological tests showed individual virus incidence of respectively 56.4%, 67.7% and 10%. Our findings corroborate with the results of Chodorska et al (2012). In order to confirm the presence of these viruses, RT-PCR assays were performed using total RNAs extracted using two silica-capture extraction procedures according to Foissac et al (2005) and specific primers targeting the coat protein genes of the various viruses. These primers, designed for the present study are (GarV-A-F: 5' YCTYTTCTCHYTDGCHTGGACYTG 3' and GarV-A-R: 5' RCCYTTCCTAGACCARTTRGCRGG 3' for GarV-A; GarV-B-F: 5' TGGGCYTGYTACCACAAYGGATC 3' and GarV-B-R 5' TCTGCGCGVGTGGADACCATRTT 3' for GarV-B; GarV-C-F: 5' ARGAYCTYTTYTCMCTYGCRTGGGC 3' and GarV-C-R: 5' GGAGGYTCRTGAATYTGTTGTTG 3' for GarV-C). The viruses were detected by a two-step RT-PCR as described by Marais et al (2015). PCRs consisted of one cycle at 95 °C for 5 min; followed by 40 cycles of denaturation at 95 °C for 45 s, annealing at 45 °C for 45 s, and elongation at 72 °C for 45s; and a final extension step at 72 °C for 10 min. Products of the expected size (214 bp for GarV-A, 363 bp for GarV-B and 439 bp for GarV-C) were amplified from 58 (88%), 47 (71%) and 56 (85%) accessions, respectively. Forty three samples (65%) were co-infected by the three viruses. Higher numbers of positives revealed by RT-PCR especially in the case of GarV-C may reflect the higher sensitivity and efficiency of this technique compared to ELISA. Direct sequencing of selected amplicons of the expected size obtained for GarV-A, -B, and -C Tunisian isolates was performed and the sequences submitted to GenBank, validating the specificity of the three RT-PCR assays. The two sequenced GarV-A isolates (MK599147 and MN995836) shared 98% nucleotide (nt) sequence identity with each other, and 93-94% identity with the closest isolate in GenBank, the “G118” isolate from China (MN059320). The three sequenced GarV-B isolates (MN995829 to MN995831) shared 88-98% nt identity with each other. For “GarV-B 18.1” (MN995830) and “GarV-B 36.2” (MN995831) the closest isolate was “1109.1” (JX682828) from Spain (92-93% nt identity). For “GarVB 17.2” (MN995829), the closest isolate was “B-Sp-3” (LC97167) from Spain (90% nt identity). The sequenced GarV-C isolate (MN995834) showed the highest sequence nt identity (93%) with the “GarV-9” isolate (HQ724848) from Spain. To our knowledge this is the first report of the presence of GarV-A, -B and -C in Tunisia. The presence of these allexiviruses may pose a threat to the preservation of the Tunisian garlic germplasm and, more broadly, to garlic production in Tunisia. For this reason, the scrupulous identification of viruses occurring in garlic plants will help to use the appropriate strategy to decrease viral incidence in garlic growing area.

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