scholarly journals Association of citrus virus A to citrus impietratura disease symptoms.

2021 ◽  
Author(s):  
Despoina Beris ◽  
Ioanna Malandraki ◽  
Nikon Vassilakos ◽  
Ioannis Theologidis ◽  
Aggeliki Rampou ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
High Throughput Sequencing ◽  
Movement Protein ◽  
Mixed Infections ◽  
Disease Symptoms ◽  
Certification Programs ◽  
Infected Tree ◽  
Characteristic Symptom ◽  
Propagation Material ◽  
Citrus Trees

Citrus impietratura disease (CID) is a graft transmissible, virus-like disease observed in old-line citrus trees; its characteristic symptom is the appearance of gum in the albedo of the affected fruits. To identify the causal agent of the disease, high throughput sequencing (HTS) was performed on symptomatic orange fruits. The analysis of the obtained data revealed in all samples, mixed infections of viroids commonly found in citrus trees together with the recently described citrus virus A (CiVA). Examination of additional symptomatic fruits with conventional RT-PCRs led to the identification of a single CiVA infection in one tree, which was verified by HTS. Indexing of the single CiVA-infected tree on indicator plants resulted in the appearance of characteristic symptoms in the leaves that were correlated with virus accumulation. Moreover, a comparative analysis among symptomatic and asymptomatic fruits derived from the same trees was performed and included the single CiVA-infected orange tree. The analysis revealed a positive correlation between the appearance of symptoms and the accumulation of CiVA RNAs. To facilitate CiVA detection during certification programs of propagation material a quantitative RT-qPCR targeting the movement protein of the virus, was developed and evaluated for reliable and sensitive detection of the virus. To the best of our knowledge this is the first study that associates CiVA with the appearance of impietratura disease symptoms.

scholarly journals Genomic Characterization and Population Structure of a Badnavirus Infecting Blackberry

Plant Disease ◽  
2017 ◽  
Vol 101 (1) ◽  
pp. 110-115 ◽  
Author(s):  
Muhammad Shafiq Shahid ◽  
Nina Aboughanem-Sabanadzovic ◽  
Sead Sabanadzovic ◽  
Ioannis E. Tzanetakis
Keyword(s):  
Population Structure ◽  
Growth Yield ◽  
Plant Genome ◽  
Disease Symptoms ◽  
Certification Programs ◽  
Double Stranded Dna ◽  
United States Population ◽  
Genomic Characterization ◽  
Putative Member ◽  
Propagation Material

Blackberry viruses are pervasive, decreasing growth, yield, and plant longevity. In a quest to identify viruses associated with blackberry yellow vein, a disease caused by virus complexes, a new double-stranded DNA virus, referred to as blackberry virus F (BVF), a putative member of the genus Badnavirus, family Caulimoviridae, was identified. The virus was found in both cultivated and wild blackberry samples collected from several states in the southern United States. Population structure, host range, and association with disease symptoms were assessed. As BVF integrates into the plant genome, it affects the production of virus-free propagation material, the cornerstone for certification programs.

scholarly journals Tomato Brown Rugose Fruit Virus Contributes to Enhanced Pepino Mosaic Virus Titers in Tomato Plants

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 879 ◽  
Author(s):  
Chen Klap ◽  
Neta Luria ◽  
Elisheva Smith ◽  
Lior Hadad ◽  
Elena Bakelman ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
High Throughput Sequencing ◽  
Amino Acid Position ◽  
Viral Disease ◽  
Mixed Infections ◽  
Rt Pcr ◽  
Tomato Production ◽  
Pepino Mosaic Virus ◽  
Disease Symptoms ◽  
Tomato Plants

The tobamovirus tomato brown rugose fruit virus (ToBRFV), a major threat to tomato production worldwide, has recently been documented in mixed infections with the potexvirus pepino mosaic virus (PepMV) CH2 strain in traded tomatoes in Israel. A study of greenhouse tomato plants in Israel revealed severe new viral disease symptoms including open unripe fruits and yellow patched leaves. PepMV was only detected in mixed infections with ToBRFV in all 104 tested sites, using serological and molecular analyses. Six PepMV isolates were identified, all had predicted amino acids characteristic of CH2 mild strains excluding an isoleucine at amino acid position 995 of the replicase. High-throughput sequencing of viral RNA extracted from four selected symptomatic plants showed solely the ToBRFV and PepMV, with total aligned read ratios of 40.61% and 11.73%, respectively, indicating prevalence of the viruses. Analyses of interactions between the co-infecting viruses by sequential and mixed viral inoculations of tomato plants, at various temperatures, showed a prominent increase in PepMV titers in ToBRFV pre-inoculated plants and in mixed-infected plants at 18–25 °C, compared to PepMV-single inoculations, as analyzed by Western blot and quantitative RT-PCR tests. These results suggest that Israeli mild PepMV isolate infections, preceded by ToBRFV, could induce symptoms characteristic of PepMV aggressive strains.

scholarly journals Graft-transmissible diseases of Ribes – pathogens, impact and control

Plant Disease ◽  
2020 ◽  
Author(s):  
Josef Spak ◽  
Igor Koloniuk ◽  
Ioannis Emmanouil Tzanetakis
Keyword(s):  
New Species ◽  
High Throughput Sequencing ◽  
Control Measures ◽  
Mixed Infections ◽  
Virus Species ◽  
New Era ◽  
Ribes Spp ◽  
And Control ◽  
Propagation Material

This article provides an up-to-date review of disease causing viruses and phytoplasmas of currants including symptoms, transmission, detection, economic impact and control measures. Currants are widely cultivated in more than 30 countries in the temperate zones of Europe, Asia, South America, Australia and New Zealand. Ribes spp. can be infected by more than 20 virus species and four Ca. Phytoplasma species, with more to be described in the future. High-throughput sequencing opened a new era of deciphering virus variants and mixed infections, leading to the characterization of several new species. The use of clean propagation material is the basis for control of Ribes graft-transmissible diseases, but this has become a challenging task given the ever-growing number of newly discovered pathogens.

Comparative analysis of paddy straw-degrading consortia in China using high-throughput sequencing

2021 ◽  
Vol 167 ◽  
pp. 104077
Author(s):  
Yunhe Ban ◽  
Xiang Li ◽  
Yuqi Li ◽  
Xinyu Li ◽  
Xu Li ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Paddy Straw

scholarly journals Discovery and Survey of a New Mandarivirus Associated with Leaf Yellow Mottle Disease of Citrus in Pakistan

Plant Disease ◽  
2020 ◽  
Vol 104 (6) ◽  
pp. 1593-1600 ◽  
Author(s):  
Jiaxing Wu ◽  
Song Zhang ◽  
Sagheer Atta ◽  
Caixia Yang ◽  
Yan Zhou ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Biological Data ◽  
High Sequence Identity ◽  
Reverse Transcription Pcr ◽  
Punjab Province ◽  
Transmission Electron ◽  
Genome Features ◽  
Yellow Mottle ◽  
Novel Virus ◽  
Citrus Trees

During biological indexing for viruses in citrus trees, in a collection of Symons sweet orange (SSO) (Citrus sinensis L. Osbeck) graft inoculated with bark tissues of citrus trees from the Punjab Province in Pakistan, several SSO trees exhibited leaf symptoms of vein yellowing and mottle. High-throughput sequencing by Illumina of RNA preparation depleted of ribosomal RNAs from one symptomatic tree, followed by BLAST analyses, allowed identification of a novel virus, tentatively named citrus yellow mottle-associated virus (CiYMaV). Genome features of CiYMaV are typical of members of the genus Mandarivirus (family Alphaflexiviridae). Virus particles with elongated flexuous shape and size resembling those of mandariviruses were observed by transmission electron microscopy. The proteins encoded by CiYMaV share high sequence identity, conserved motifs, and phylogenetic relationships with the corresponding proteins encoded by Indian citrus ringspot virus (ICRSV) and citrus yellow vein clearing virus (CYVCV), the two current members of the genus Mandarivirus. Although CYVCV is the virus most closely related to CiYMaV, the two viruses can be serologically and biologically discriminated from each other. A reverse-transcription PCR method designed to specifically detect CiYMaV revealed high prevalence (62%) of this virus in 120 citrus trees from the Punjab Province, Pakistan, where the novel virus was found mainly in mixed infection with CYVCV and citrus tristeza virus. However, a preliminary survey on samples from 200 citrus trees from the Yunnan Province, China failed to detect CiYMaV in this region, suggesting that the molecular, serological, and biological data provided here are timely and can help to prevent the spread of this virus in citrus-producing countries.

scholarly journals Virus and virus-like diseases of grapevine in Hungary

2011 ◽  
Vol 17 (3) ◽  
Author(s):  
J. Lázár ◽  
Gy. D. Bisztray
Keyword(s):  
Energy Metabolism ◽  
Host Cell ◽  
Particle Morphology ◽  
Plant Viruses ◽  
Diagnostic Methods ◽  
Economic Damage ◽  
Mixed Infections ◽  
Disease Symptoms ◽  
The World

Viruses and viroids are submicroscopic infectious particles which can cause disease symptoms on grapevine. These parasites are depending completely on the energy metabolism of the plant cell. To enter the host cell plant viruses depend on injuries or on transmission via invertebrates (insects, nematodes, etc.). Viruses are classified by many characters including particle morphology, host range and information content of the genome. At present about 70 viruses including 7 viroids infecting grapevine are known. In single or mixed infections they are potentially detrimental to the quality and quantity of grape production in any growing area of the world. Some viruses can cause severe economic damage in vineyards. In Hungary many important viruses and viroids have been detected in grape. This review summarises characteristics of viruses and the results of detection and characterization of virus and virus like diseases of grapevine in Hungary. The identification of the causal agent, its transmission, geographical distribution and the development of the diagnostic methods are also discussed.

scholarly journals High-Throughput Sequencing Identifies Novel Viruses in Nectarine: Insights to the Etiology of Stem-Pitting Disease

2016 ◽  
Vol 106 (5) ◽  
pp. 519-527 ◽  
Author(s):  
D. E. V. Villamor ◽  
T. A. Mekuria ◽  
S. S. Pillai ◽  
K. C. Eastwell
Keyword(s):  
High Throughput ◽  
Pathogen Detection ◽  
High Throughput Sequencing ◽  
Prunus Persica ◽  
Disease Symptoms ◽  
Testing Procedures ◽  
Molecular Tests ◽  
Putative Member ◽  
Stem Pitting ◽  
Virus Testing

Recent studies have shown the superiority of high-throughput sequencing (HTS) technology over many standard protocols for pathogen detection. HTS was initiated on fruit tree accessions from disparate sources to improve and advance virus-testing procedures. A virus with genomic features resembling most closely that of the recently described Nectarine stem-pitting-associated virus, putative member of genus Luteovirus, was found in three nectarine trees (Prunus persica cv. nectarina), each exhibiting stem-pitting symptoms on the woody cylinder above the graft union. In these samples, HTS also revealed the presence of a coinfecting virus with genome characteristics typical of members of the genus Marafivirus. The same marafivirus- and luteovirus-like viruses were detected in nonsymptomatic nectarine and peach selections, indicating only a loose relationship between these two viruses with nectarine stem-pitting disease symptoms. Two selections infected with each of these viruses had previously tested free of known virus or virus-like agents using the current biological, serological, and molecular tests employed at the Clean Plant Center Northwest. Overall, this study presents the characterization by HTS of novel marafivirus- and luteovirus-like viruses of nectarine, and provides further insights into the etiology of nectarine stem-pitting disease. The discovery of these new viruses emphasizes the ability of HTS to reveal viruses that are not detected by existing protocols.

Small RNA and transcriptome sequencing of a symptomatic peony plant reveals mixed infections with novel viruses

Plant Disease ◽  
2021 ◽  
Author(s):  
Anning Jia ◽  
Chenge Yan ◽  
Hang Yin ◽  
Rui Sun ◽  
Fei Xia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Viral Infections ◽  
Triple Gene Block ◽  
Field Investigation ◽  
Mixed Infections ◽  
Species Classification ◽  
Gene Block ◽  
Sequence Identity

To identify the viruses in tree peony plants associated with the symptoms of yellowing, leaf rolling, stunted growth, and decline, high-throughput sequencing of small RNA and mRNA was conducted from a single symptomatic plant. Bioinformatic analyses and reconstruction of viral genomes indicated mixed viral infections involving cycas necrotic stunt virus (CNSV), apple stem grooving virus (ASGV), lychnis mottle virus (LycMoV), grapevine line pattern virus (GLPV), and three new viruses designated as peony yellowing-associated citrivirus (PYaCV, Citrivirus in Betaflexiviridae), peony betaflexivirus 1 (PeV1, unclassified in Betaflexiviridae), and peony leafroll-associated virus (PLRaV, Ampelovirus in Closteroviridae). PYaCV was 8,666 nucleaotides (nt) in length, comprising three open reading frames (ORFs) and shared 63.8–75.9% nucleotide sequence identity with citrus leaf blotch virus (CLBV) isolates. However, the ORF encoding the replication-associated protein (REP) shared 57% and 52% sequence identities at the nt and amino acid (aa) level, respectively, with other reported CLBV isolates, which were below the criterion for species classification within the family Betaflexiviridae. Recombination analysis identified putative recombination sites in PYaCV, which originated from CLBV. PeV1, only identified from the transcriptome data, was 8,124 nt in length with five ORFs encoding the REP (ORF1), triple gene block (TGB, ORF2–4) and coat protein (CP, ORF5) proteins. Phylogenetic analysis and sequence comparison showed that PeV1 clustered with an unassigned member, the garlic yellow mosaic-associated virus (GYMaV) within the Betaflexiviridae family, into a separate clade. Partial genome sequence analysis of PLRaV (12,545 nt) showed it contained seven ORFs encoding the partial polyprotein 1a, the RNA-dependent RNA polymerase (RdRp), two small hydrophobic proteins p11 and p6, HSP70h, p55, and a CP duplicate, which shared low aa sequence identity with Closteroviridae family members. Phylogenetic analysis based on the aa sequences of RdRp or HSP70h indicated that PLRaV clustered with grapevine leafroll-associated virus 1 (GLRaV-1) and GLRaV-13 in the Ampelovirus genus. Field investigation confirmed the wide distribution of these viruses, causing mixed infections of peony plants in Beijing.

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