Syrah decline virus

This disease, known as "Syrah decline," is a growing concern to the multi-million dollar Syrah segment of the California wine industry. A related disease has been on the rise in French vineyards as well. Up until now, the pathogenicity, histological, graft incompatibility and genetic studies did not produce any conclusive results or insights into the cause of this syndrome.

This investigation into the decline of Syrah grapevines is led by Dr. Adib Rowhani, UC Davis, as part of the university's ongoing research into California grape production and vineyard management.

Eureka Genomics will continue to be involved in the project. The study was based on Eureka Genomics' proprietary next-generation sequencing data analysis technology. An Illumina Genome Analyzer was used to generate sequencing reads. Viacheslav Fofanov, director of bioinformatics at Eureka Genomics, then compared 5. Sequences unique to the diseased sample were assembled, and using the BLAST search algorithm, homologous sequences were identified by comparison of the assembled contigs to the GenBank database.

These identified sequences were sorted into pathogen and parasite classes. Among the viral species identified, a mixed infection of Grapevine rupestris stem-pitting-associated foveavirus strains was described as containing at least two novel members.

Complete genome characterization and coat protein genealogy of isolates of maize dwarf mosaic virus from johnsongrass and maize in Oklahoma and Missouri. Gell, G. Genetic diversity of Hungarian Maize dwarf mosaic virus isolates.

Virus Genes 40 2 , — Chung, B. An overlapping essential gene in the Potyviridae. Kong, P. Complete nucleotide sequence and analysis of the putative polyprotein of maize dwarf mosaic virus genomic RNA Bulgarian isolate.

Rozas, J. Bioinformatics 19 , — Candresse, T. Appearances can be deceptive: Revealing a hidden viral infection with deep sequencing in a plant quarantine context. Brunt, A. The population genetics of maize dwarf mosaic virus in Spain. Tobias, I. Comparison of Hungarian and Bulgarian isolates of maize dwarf mosaic virus.

Cereal Res. An unusual feature at the N-terminal end of the coat protein of maize dwarf mosaic virus isolated in Hungary. Stewart, L. Viruses in maize and johnsongrass in southern Ohio. Phytopathology 12 , — Ali, A. Early season survey of pea viruses in Pakistan and the detection of two new pathotypes of pea seedborne mosaic potyvirus.

Occurrence of viruses infecting watermelon, other cucurbits, and weeds in the parts of southern United States. Rapid and efficient purification of Cowpea chlorotic mottle virus by sucrose cushion ultracentrifugation.

Methods , 84—86 Sambrook, J. Thompson, J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. Librado, P. Bioinformatics 25 11 , — Pond, S. HyPhy: Hypothesis testing using phylogenies. Bioinformatics 21 , — Nei, M. Book Google Scholar.

Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 3 , — Fu, Y. Statistical tests of neutrality of mutations. Genetics 3 , Wright, S. Genetical structure of populations. Nature , — Martin, D. RDP4: Detection and analysis of recombination patterns in virus genomes.

Virus Evol. Masumi, M. Complete genome sequences maize dwarf mosaic and sugarcane mosaic virus isolates co-infecting maize in Spain. Download references. You can also search for this author in PubMed Google Scholar. Both authors read and approved the final version of the manuscript. Correspondence to Akhtar Ali. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material.

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Skip to main content Thank you for visiting nature. Download PDF. Subjects Diseases Medical research Urology. Abstract Next-generation sequencing is a robust approach to sequence plant virus genomes in a very short amount of time compared to traditional sequencing methods. Introduction Next-generation sequencing NGS has been frequently used for plant virology studies since 1 , 2 , 3 and is gaining rapid recognition for discovering entire novel viral sequences and obtaining complete genome sequences for known and unknown viruses in a short period of time 4 , 5.

Figure 1. Full size image. Figure 2. Full size table. Figure 3. Figure 4. Table 4 Population based analysis of genetic parameters for individual coding region of 28 MDMV isolates. Discussion Within the span of 40 years, DNA sequencing has improved dramatically. In nature, potyviruses are transmitted by aphids in a non-persistent manner, which is one of the reasons why they cause serious disease epidemics in a wide range of cultivated plants Ng and Perry Those motifs have been considered to play vital roles in aphid transmission of potyviruses Revers and Garcia However, even though all these conserved motifs are present, aphid transmission demands species-specific interactions Gibbs et al.

Further examination is needed to identify which aphid species can transmit PalMV. Importantly, these maize-infecting potyviruses were found to cause maize lethal necrosis disease MLND when synergistic co-infection with maize chlorotic mottle virus MCMV Scheets ; Stenger et al. Furthermore, in this study, PalMV-infected millet plants showed serious dwarfing and mosaic symptom during early growth stages, resulting in inability to flowering, which would seriously damage crop yield and quality.

Further studies are intended to evaluate the potential impact of PalMV on the growth and production of some cereal crops. The host adaptation of some potyviruses may be due to P1 protein, the most divergent ones in terms of length and aa sequence among the 11 mature proteins Valli et al. P1 self-cleavage activity is indispensable for both potyviral viability and host range specificity Valli et al.

It is assumed that P1 protein has a similar effect in determining the host range of PalMV. Hence, not only the actual host range of PalMV, but also the relationship between PalMV infection and mosaic symptom are yet to be investigated in the future.

It is widely known that credible and effective diagnosis of plant viruses is very crucial for generating disease management strategy. Meanwhile, this molecular test should be useful in supervising viral distribution and epidemiology Marais et al. In conclusion, the biological, pathological and molecular data we obtained here support that PalMV is assigned to a distinct new species within the genus Potyvirus.

Members of Potyvirus are distributed worldwide and cause severe losses on crops. Although limited numbers of potyviruses have been reported in monocots, cereal-infecting potyviruses pose great damage on grain production.

In this study, we proved that maize, millet, wheat, sorghum and rice were experimentally infected by PalMV via rub inoculation, suggesting that PalMV is a potentially dangerous virus for a wide range of cereal crops.

Considering the danger to cereal crops posed by PalMV, we report it for the development of disease control strategies in the future. Pennisetum plants showing severe leaf chlorosis and growth abnormalities particularly severe dwarfism and delayed flowering were sampled, and the potential viral agent was maintained by periodical sap inoculation of the diseased Pennisetum on the first true leaves of maize Z.

For inoculation experiments, crude virus extracts were prepared by homogenizing the symptomatic maize leaf tissues in 0. Plant sap was filtered and the crude extracts were rub-inoculated individually to the tested plant leaves. For mock control, plants were inoculated with phosphate buffer.

Carborundum was utilized as an abrasive, and the inoculated leaves were rinsed with double distilled H 2 O ddH 2 O to remove impurities. After inoculation, the plants were kept in a greenhouse under natural conditions for symptom development Dijkstra and de Jager, ; Addy et al. Virus particles were isolated from systemically infected maize leaves following the method for filamentous virion purification Dijkstra and de Jager, We obtained crude purified virus particles from the supernatant.

Virus yield in purified preparation was estimated spectrophotometrically Hema et al. Viral RNA was extracted from purified virus particles according to the previous methods Dijkstra and de Jager, ; Zhu et al. To confirm the full genome of the virus associated with P. The primers were utilized to obtain the gaps between the various contigs and terminal untranslated region sequences.

Overlapping sequences were assembled using Seqman Pro 7. All nt and aa sequences used in sequence comparisons and phylogenetic analyses were retrieved from GenBank database Additional file 2 : Table S2. Average pairwise distances were computed using MEGA7. Phylogenetic trees were constructed using the Neighbor-joining method with strict nt or aa distances and randomized bootstrapping evaluation of branching validity using MEGA7.

The robustness of the inferred evolutionary relationships was assessed by bootstrap replicates Kumar et al. The amplified fragments were subjected to agarose gel electrophoresis and then visualized in UV illuminator after ethidium bromide staining.

Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol Plant Pathol. Aiyar A. Methods Mol Biol. Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Barnett OW. A summary of potyvirus taxonomy and definitions. Arch Virol Suppl.

An overlapping essential gene in the Potyviridae. Cui H, Wang A. The biological impact of the hypervariable N-terminal region of potyviral genomes. Annu Rev Virol. A previously undescribed potyvirus isolated and characterized from arborescent Brugmansia. Arch Virol. Dijkstra J, de Jager CP. Practical plant virology: protocols and exercises. Heidelberg: Springer; Book Google Scholar. Molecular characterization of a distinct potyvirus from whitegrass in China.

The prehistory of potyviruses: their initial radiation was during the dawn of agriculture. PLoS One. Gotz R, Maiss E. The complete sequence of the genome of Cocksfoot streak virus CSV , a grass infecting potyvirus. Next-generation sequencing and genome editing in plant virology. Front Microbiol. Molecular characterization and interviral relationships of a flexuous filamentous virus causing mosaic disease of sugarcane Saccharum officinarum L.

A new corn disease in Ohio. Plant Dis Rep. Google Scholar. Nucleic Acids Res. Kaliciak A, Syller J. Eur J Plant Pathol. Article Google Scholar. Improving methane production from anaerobic digestion of Pennisetum Hybrid by alkaline pretreatment.

Bioresour Technol. Detection of viruses in sweetpotato from Honduras and Guatemala augmented by deep-sequencing of small-RNAs. Plant Dis. MEGA7: molecular evolutionary genetics analysis version 7. Mol Biol Evol. Molecular characterization of a novel potyvirus infecting noni. Virus taxonomy: the database of the international committee on taxonomy of viruses ICTV. Molecular toxicology protocols. Methods in molecular biology, vol.

New York: Humana; Chapter Google Scholar. PubMed Article Google Scholar. Virus variants with differences in the P1 protein coexist in a Plum pox virus population and display particular host-dependent pathogenicity features.

Virus infection in remnant native bunchgrasses from invaded California grasslands. New Phytol. Characterization by deep sequencing of Prunus virus T , a novel tepovirus infecting prunus species.