Sequence Comparison and Phylogeny of Nucleotide Sequence of Coat Protein and Nucleic Acid Binding Protein of a Distinct Isolate of Shallot virus X from India

Majumder, S.

doi:10.1007/s13337-011-0040-5

Cited by 7 publications

(4 citation statements)

References 12 publications

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“…The present study was motivated by reports of a yellow stripe disease on shallot be significantly more distant from "classical" isolates, and define a new phylogenetic cluster, providing evidence for a wider diversity than previously known [24]. Similarly, three complete genome sequences (near-complete for one) of SLV were determined through this study, representing isolates from a new phylogenetic cluster and extending the known diversity range of this virus.…”

Section: Discussionmentioning

confidence: 92%

Characterization of the virome of shallots affected by the shallot mild yellow stripe disease in France

Marais

Faure

Theil

et al. 2019

Preprint

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To elucidate the etiology of a new disease on shallot in France, double-stranded RNAs from asymptomatic and symptomatic shallot plants were analyzed by high-throughput sequencing (HTS). Contigs annotation, molecular characterization and phylogenetic analyses revealed the presence in symptomatic plants of a virus complex consisting of shallot virus X (ShVX, Allexivirus), shallot latent virus (SLV, Carlavirus) and two novel viruses belonging to the genera Carlavirus and Potyvirus, for which the names of shallot virus S (ShVS) and shallot mild yellow stripe associated virus (SMYSaV), are proposed. Complete or near complete genomic sequences were obtained for all these agents, revealing divergent isolates of ShVX and SLV. Trials to fulfill Koch’s postulates were pursued but failed to reproduce the symptoms on inoculated shallots, even though the plants were proved to be infected by the four viruses detected by HTS. Replanting of bulbs from SMYSaV-inoculated shallot plants resulted in infected plants, showing that the virus can perpetuate the infection over seasons. A survey analyzing 351 shallot samples over a four years period strongly suggests an association of SMYSaV with the disease symptoms. An analysis of SMYSaV diversity indicates the existence of two clusters of isolates, one of which is largely predominant in the field over years.The sequences reported in the present manuscript have been deposited in the GenBank database under accession numbers MG571549, MH292861, MH389247 to MH389255, and MG910501 to MG910598.

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Section: Discussionmentioning

confidence: 92%

Characterization of the virome of shallots affected by the shallot mild yellow stripe disease in France

Marais

Faure

Theil

et al. 2019

Preprint

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“…A CDD database search of BdBV1 P5 revealed that it contains a Flexi_CP super family protein domain (accession no. cl02836 , E -value = 5.71e-45) commonly found in the of potexviruses and carlaviruses ( Majumder and Baranwal, 2011 ). In addition, alignment of BdBV1 ORF5 and CP sequences of other related viruses revealed the presence of a putative salt bridge ( Figure 1C ), which was reported as the hydrophobic core in flexuous, rod-shaped ssRNA plant viruses ( Dolja et al, 1991 ).…”

Section: Resultsmentioning

confidence: 99%

Discovery and Characterization of a Novel Bipartite Botrexvirus From the Phytopathogenic Fungus Botryosphaeria dothidea

et al. 2021

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In this study, we describe a novel positive, single-stranded (+ss) RNA mycovirus, named Botryosphaeria dothidea botrexvirus 1 (BdBV1), from a phytopathogenic fungus Botryosphaeria dothidea showing abnormal morphology and attenuated virulence. BdBV1 is phylogenetically related to Botrytis virus X (BotVX) and is the second potential member of the proposed genus Botrexvirus in the family Alphaflexiviridae. However, it differs from the monopartite BotVX in that BdBV1 possesses a bipartite genome comprised of two ssRNA segments (RNA1 and RNA2 with lengths of 5,035 and 1,063 nt, respectively). BdBV1 RNA1 and RNA2 encode putative RNA-dependent RNA polymerase (RdRp) and coat protein (CP) genes, which share significant identity with corresponding genes in both fungal and plant viruses. Moreover, open reading frames (ORFs) 2–4 of BdBV1 RNA1 shared no detectable identity with any known viral proteins. Immunosorbent electron microscopy (ISEM) analysis using an antibody against the virus CP generated in vitro revealed that BdBV1 is encapsidated in filamentous particles. A comparison of the biological effects of BdBV1 infection on symptoms and growth in isogenic lines of virus-free and virus-infected B. dothidea revealed that BdBV1 is probably involved in reduced growth and virulence of the host fungus. This study describes and characterizes a novel bipartite botrexvirus, which is closely related to uni- and multi-partite fungal and plant viruses and contributes useful information to a better understanding of virus evolution.

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“…It is a member of the Alliaceae family and is closely related to onion, garlic and chives. It is mainly grown in China, Southeast Asia, and Europe [ 1 ]. The multiplier onion is considered more nutritive than a bigger variety in terms of carbohydrates, protein, carotene and minerals [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

Whole genome sequence analysis of shallot virus X from India reveals it to be a natural recombinant with positive selection pressure

Singh,

Teotia,

Singh

et al. 2024

BMC Genom Data

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Background Shallots are infected by various viruses like Onion yellow dwarf virus (OYDV), Leek yellow stripe virus (LYSV), Shallot latent virus (SLV) and Shallot virus X (ShVX). In India, they have been found to be persistently infected by ShVX. ShVX also infects onion and garlic in combination with other carlaviruses and potyviruses. ShVX is a member of genus Allexivirus of family Alphaflexiviridae. ShVX has a monopartite genome, which is represented by positive sense single-stranded RNA. Globally, only six complete and 3 nearly complete genome sequences of ShV X are reported to date. This number is insufficient to measure a taxon’s true molecular diversity. Moreover, the complete genome sequence of ShVX from Asia has not been reported as yet. Therefore, this study was undertaken to generate a complete genome sequence of ShVX from India. Results Shallot virus X (ShVX) is one of the significant threats to Allium crop production. In this study, we report the first complete genome sequence of the ShVX from India through Next-generation sequencing (NGS). The complete genome of the ShVX (Accession No. OK104171), from this study comprised 8911 nucleotides. In-silico analysis of the sequence revealed variability between this isolate and isolates from other countries. The dissimilarities are spread all over the genome specifically some non-coding intergenic regions. Statistical analysis of individual genes for site-specific selection indicates a positive selection in NABP region. The presence of a recombination event was detected in coat protein region. The sequence similarity percentage and phylogenetic analysis indicate ShVX Indian isolate is a distinctly different isolate. Recombination and site-specific selection may have a function in the evolution of this isolate. This is the first detailed study of the ShVX complete genome sequence from Southeast Asia. Conclusion This study presents the first report of the entire genome sequence of an Indian isolate of ShVX along with an in-depth exploration of its evolutionary traits. The findings highlight the Indian variant as a naturally occurring recombinant, emphasizing the substantial role of recombination in the evolution of this viral species. This insight into the molecular diversity of strains within a specific geographical region holds immense significance for comprehending and forecasting potential epidemics. Consequently, the insights garnered from this research hold practical value for shaping ShVX management strategies and providing a foundation for forthcoming studies delving into its evolutionary trajectory.

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Sequence Comparison and Phylogeny of Nucleotide Sequence of Coat Protein and Nucleic Acid Binding Protein of a Distinct Isolate of Shallot virus X from India

Cited by 7 publications

References 12 publications

Characterization of the virome of shallots affected by the shallot mild yellow stripe disease in France

Characterization of the virome of shallots affected by the shallot mild yellow stripe disease in France

Discovery and Characterization of a Novel Bipartite Botrexvirus From the Phytopathogenic Fungus Botryosphaeria dothidea

Whole genome sequence analysis of shallot virus X from India reveals it to be a natural recombinant with positive selection pressure

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