Complete nucleotide sequence of an Argentinean isolate of sweet potato virus G

Pardina, P. E. Rodríguez; Bejerman, Nicolás; Luque, A. V.; Feo, L. Di

doi:10.1007/s11262-012-0784-z

Cited by 15 publications

(6 citation statements)

References 23 publications

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“…Viral genomic RNA or DNA packaged in viral particles is protected from DNase and RNase treatments. Therefore, enrichment of VLPs (Figure 1) and fecal samples (20,52,64,96) as well as in several studies of plant samples (12,27,28,36,79,81,93). VLP preparations contain contaminating mitochondria and bacteria, so VLPs are often treated with chloroform to disrupt mitochondrial and bacterial membranes before nuclease digestion and the extraction of VLP-associated nucleic acids for deep sequencing (51,100).…”

Section: Sample Preparation: Strategies To Enrich Virus Sequencesmentioning

confidence: 99%

Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms

Ding

Zhang

et al. 2015

Annu. Rev. Phytopathol.

185

135

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A fast, accurate, and full indexing of viruses and viroids in a sample for the inspection and quarantine services and disease management is desirable but was unrealistic until recently. This article reviews the rapid and exciting recent progress in the use of next-generation sequencing (NGS) technologies for the identification of viruses and viroids in plants. A total of four viroids/viroid-like RNAs and 49 new plant RNA and DNA viruses from 18 known or unassigned virus families have been identified from plants since 2009. A comparison of enrichment strategies reveals that full indexing of RNA and DNA viruses as well as viroids in a plant sample at single-nucleotide resolution is made possible by one NGS run of total small RNAs, followed by data mining with homology-dependent and homology-independent computational algorithms. Major challenges in the application of NGS technologies to pathogen discovery are discussed.

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Section: Sample Preparation: Strategies To Enrich Virus Sequencesmentioning

confidence: 99%

Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms

Ding

Zhang

et al. 2015

Annu. Rev. Phytopathol.

185

135

View full text Add to dashboard Cite

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“…However, it was also found in Peru ( Untiveros et al, 2008 ), Vietnam ( Ha et al, 2008 ), Easter Island ( Rännäli et al, 2009 ) and recently in China ( Qin et al, 2013 ). The other potyviruses infecting sweet potato (SPVG, SPLV, and SPV2) have been poorly studied; however, their complete genome sequences were recently reported and compared to SPFMV ( Li et al, 2012a ; Rodriguez Pardina et al, 2012 ; Wang et al, 2013 ). Similar to SPFMV, SPLV was reported to cause synergistic disease when coinfected with SPCSV ( Untiveros et al, 2007 ).…”

Section: Discussionmentioning

confidence: 99%

The Current Incidence of Viral Disease in Korean Sweet Potatoes and Development of Multiplex RT-PCR Assays for Simultaneous Detection of Eight Sweet Potato Viruses

Kwak

Kim

Shin

et al. 2014

The Plant Pathology Journal

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Sweet potato is grown extensively from tropical to temperate regions and is an important food crop worldwide. In this study, we established detection methods for 17 major sweet potato viruses using single and multiplex RT-PCR assays. To investigate the current incidence of viral diseases, we collected 154 samples of various sweet potato cultivars showing virus-like symptoms from 40 fields in 10 Korean regions, and analyzed them by RT-PCR using specific primers for each of the 17 viruses. Of the 17 possible viruses, we detected eight in our samples. Sweet potato feathery mottle virus (SPFMV) and sweet potato virus C (SPVC) were most commonly detected, infecting approximately 87% and 85% of samples, respectively. Furthermore, Sweet potato symptomless virus 1 (SPSMV-1), Sweet potato virus G (SPVG), Sweet potato leaf curl virus (SPLCV), Sweet potato virus 2 ( SPV2), Sweet potato chlorotic fleck virus (SPCFV), and Sweet potato latent virus (SPLV) were detected in 67%, 58%, 47%, 41%, 31%, and 20% of samples, respectively. This study presents the first documented occurrence of four viruses (SPVC, SPV2, SPCFV, and SPSMV-1) in Korea. Based on the results of our survey, we developed multiplex RT-PCR assays for simple and simultaneous detection of the eight sweet potato viruses we recorded.

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“…A further advantage of the metagenomic strategies is the detection of plant-associated viral sequences, even at low concentrations in their host tissues [13]. A wide range of protocols for enriching virus particles have been used, and several viruses have been detected and characterized after employing these approaches [14][15][16][17][18]. However, the metagenomic characterization of viruses and viroids in tree species is limited to species into the genera of high economic relevance such as Prunus, Pyrus, Malus, Citrus, Actidinia, Diospyros, Morus, and Vitis [19][20][21].…”

Section: Introductionmentioning

confidence: 99%

Molecular Characterization of Hovenia Dulcis-Associated Virus 1 (HDaV1) and 2 (HDaV2): New Tentative Species within the Order Picornavirales

Nery

Melo

Boiteux

et al. 2020

Viruses

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In a systematic field survey for plant-infecting viruses, leaf tissues were collected from trees showing virus-like symptoms in Brazil. After viral enrichment, total RNA was extracted and sequenced using the MiSeq platform (Illumina). Two nearly full-length picorna-like genomes of 9534 and 8158 nucleotides were found associated with Hovenia dulcis (Rhamnaceae family). Based upon their genomic information, specific primers were synthetized and used in RT-PCR assays to identify plants hosting the viral sequences. The larger contig was tentatively named as Hovenia dulcis-associated virus 1 (HDaV1), and it exhibited low nucleotide and amino acid identities with Picornavirales species. The smaller contig was related to insect-associated members of the Dicistroviridae family but exhibited a distinct genome organization with three non-overlapping open reading frames (ORFs), and it was tentatively named as Hovenia dulcis-associated virus 2 (HDaV2). Phylogenetic analysis using the amino acid sequence of RNA-dependent RNA polymerase (RdRp) revealed that HDaV1 and HDaV2 clustered in distinct groups, and both viruses were tentatively assigned as new members of the order Picornavirales. HDaV2 was assigned as a novel species in the Dicistroviridae family. The 5′ ends of both viruses are incomplete. In addition, a nucleotide composition analysis (NCA) revealed that HDaV1 and HDaV2 have similarities with invertebrate-infecting viruses, suggesting that the primary host(s) of these novel virus species remains to be discovered.

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Complete nucleotide sequence of an Argentinean isolate of sweet potato virus G

Cited by 15 publications

References 23 publications

Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms

Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms

The Current Incidence of Viral Disease in Korean Sweet Potatoes and Development of Multiplex RT-PCR Assays for Simultaneous Detection of Eight Sweet Potato Viruses

Molecular Characterization of Hovenia Dulcis-Associated Virus 1 (HDaV1) and 2 (HDaV2): New Tentative Species within the Order Picornavirales

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