Discovery of Viruses and Virus-Like Pathogens in Pistachio using High-Throughput Sequencing

Rwahnih, Maher Al; Rowhani, Adib; Westrick, Nathaniel M.; Stevens, Kristian; Diaz‐Lara, Alfredo; Trouillas, Florent P.; Preece, John E.; Kallsen, Craig E.; Farrar, K.; Golino, Deborah A.

doi:10.1094/pdis-12-17-1988-re

Cited by 52 publications

(33 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Here, separate aliquots of the six samples of total RNAs were prepared and each subjected to ribosomal RNA depletion and subsequent cDNA library construction using a TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina, San Diego, CA). All six samples were then sequenced on the Illumina NextSeq 500 platform as previously described (Al Rwahnih et al, 2018).…”

Section: Acp-associated Virus Screenings With Rt-pcr and Pcrmentioning

confidence: 99%

“…The resulting Illumina reads were subjected to adapter trimming and de novo assembled into contiguous consensus sequences (contigs) with size lengths of at least 200 base pairs by CLC Bio Genomic Workstation (v8.5.1; Qiagen, Hilden, Germany). These contigs were then annotated by a multistep process for generation of candidate viral sequences as previously described (Al Rwahnih et al, 2018). The first group of contigs was generated with the tBLASTx program (v. 2.4.0) for comparison of sample contig sequences against the viral genome database of the NCBI Refseq (https://www.ncbi.nlm.nih.gov/genome/ viruses/) (Tatusova and Madden, 1999).…”

Section: Assembly and Sequence Analysismentioning

confidence: 99%

See 1 more Smart Citation

The Detection and Surveillance of Asian Citrus Psyllid (Diaphorina citri)—Associated Viruses in Florida Citrus Groves

et al. 2020

Self Cite

View full text Add to dashboard Cite

The plant pathogenic bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent of the citrus disease Huanglongbing (HLB), and its insect vector, the Asian citrus psyllid (ACP; Diaphorina citri), have been devastating the Florida citrus industry. To restore the competitive production presence of Florida in the worldwide citrus market, effective and sustainable control of HLB and the ACP needs to be identified. As alternatives for resistance-inducing insecticides, viruses are currently being considered for biological control of the ACP. To identify possible biological control candidates, we conducted one of the most comprehensive surveys of natural ACP populations in major citrus production regions spanning 21 counties in Florida. By optimizing PCRs and RT-PCRs, we were able to successfully detect and monitor the prevalence of five previously identified ACPassociated RNA and DNA viruses throughout Florida citrus groves, which include: Diaphorina citri-associated C virus (DcACV), Diaphorina citri flavi-like virus (DcFLV), Diaphorina citri densovirus (DcDNV), Diaphorina citri reovirus (DcRV), and Diaphorina citri picorna-like virus (DcPLV). Adult and nymph ACP populations from 21 of Florida's major citrus-producing counties were collected each month during approximately 18 consecutive months. RNA extracts used for these viral screens were also regionally combined and subjected to High Throughput Sequencing (HTS) to reveal a more comprehensive picture of known and unknown viruses in Florida ACP populations. We discovered that DcACV was the most prevalent ACP-associated virus throughout nymph and adult ACP populations in Florida, detected in more than 60% of all samples tested, followed by DcPLV and DcFLV. HTS allowed us to identify a novel ACP-associated reolike virus and a picorna-like virus. The putative reo-like virus, tentatively named Diaphorina citri cimodo-like virus, was later surveyed and detected back in seasonal adult and nymph ACP samples collected in Florida during this study. HTS generated data also revealed that the most abundant virus in Florida ACP populations was Citrus tristeza virus (CTV), which is not an ACP-associated virus, suggesting persistent presence of CTV infection in citrus throughout Florida groves. Collectively, information obtained from our study may be able

show abstract

Section: Acp-associated Virus Screenings With Rt-pcr and Pcrmentioning

confidence: 99%

Section: Assembly and Sequence Analysismentioning

confidence: 99%

The Detection and Surveillance of Asian Citrus Psyllid (Diaphorina citri)—Associated Viruses in Florida Citrus Groves

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…In order to explore the distribution of GVL, we gathered data from grapevine samples from Croatia The sample from USA corresponded to a quarantine selection Katelin (KA), which was received in the positive sample was high-throughput sequenced and the obtained ca. 11.5 million raw reads were filtered and de novo assembled with parameters described in Al Rwahnih et al 2018 [16]. A contig with high similarity with GVL was identified by BLAST and subsequently refined, resulting in a 7,591 nt virus draft genome (GVL-KA, MH643739), sharing the genomic architecture and a 97.9% nt identity with GVL-RI (Supp .…”

Section: Resultsmentioning

confidence: 99%

“…screenhouse and assayed for known grapevine viruses as described previously[16]. In addition, total RNA from…”

mentioning

confidence: 99%

Grapevine virus L: a Novel Vitivirus in Grapevine

Debat

Zavallo²,

Brisbane³

et al. 2018

Preprint

View full text Add to dashboard Cite

Vitivirus is a genus within the family Betaflexiviridae (Tymovirales) of ssRNA(+) viruses. There are currently ten ICTV recognized virus species in the genus; nevertheless, the extended use of NGS technologies is rapidly expanding their diversity and six more have been proposed recently. Here, we present the in silico characterization of a novel virus detected in grapevine (cv Riesling) which fits the genomic architecture and evolutionary constraints to be classifiable within the Vitivirus genus. The detected virus sequence is 7,607 nt long, including a typical genome organization of ORFs encoding a replicase (RP), a 22 kDa protein, a movement protein, a coat protein (CP) and a nucleic acid binding protein. Phylogenetic insights based on the predicted RP and CP, which share a 70.2% and 78.2% identity with its closest neighbour's grapevine virus E proteins, unequivocally clusters the identified virus within the Vitivirus genus. Multiple independent RNAseq data confirmed the presence of the detected virus in berries at diverse developmental stages. We tentatively propose the name grapevine virus L (GVL) to the detected putative Vitivirus. KeywordsVitivirus, Grapevine, cv Riesling, virus discovery, Betaflexiviridae Accession numberGrapevine virus L sequence (GVL-rs) has been deposited in GenBank under accession number MH248020. CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/314674 doi: bioRxiv preprint first posted online May. 4, 2018; ReportVitiviruses present flexuous, non-enveloped, filamentous virus particles of 725-785 nm and 12 nm length and diameter. Their nucleocapsid is cross-banded and striated diagonally. They have a linear ssRNA(+) genome (~7.3-7.6 kb), with a methylated nucleotide cap at the 5' end and a 3' poly (A) tail [1]. There are ten species of vitiviruses recognized by the ICTV, nevertheless, just in the last six months, six new species have been proposed, five of them infecting grapevine [2][3][4][5][6]. Grapevine is their most prevalent natural host but they have also been found to infect several crops such as Mint (Mentha x glaciaris), arracacha (Arracacia xanthorrhiza) blue agave (Agave tequilana) and kiwi (Actinidia chinense) [7][8][9].Vitiviruses appear to be latent in Vitis vinífera cultivars, and so far, only Grapevine virus A and Grapevine virus B had been consistently associated to grapevine diseases of the rugose wood complex (Grapevine vitiviruses) or Shiraz disease (reviewed by Minafra [10]). The etiological role of the recently described vitiviruses should be assessed in order to establish its relationships with known or unknown viral diseases. The synergistic effects between vitiviruses and other grapevine viruses appears to be significant [11]. The availability of complete sequences of these viruses could allow the development of full-length infectious clones, and ...

show abstract

“…It has been proven after fish koi obtained from Blitar, after 3 days maintenance, there are 7 koi fish herpes viruses were identified, characterized with characteristic features physical on fish, similar with the experiment before (Figure 1). Rwahnih et al, 2018). Virus nomenclature can base on manifestation morphology, pathogenesis or the effect off manifestation clinical, type animals used as host, antigenic properties, growth characteristics, type of cytopathic influence on cell culture or based on homology with other viruses that have already known (Waltzek et al, 2005).…”

Section: Visual Measurementmentioning

confidence: 99%

Identification of Koi Herpesvirus on Fish Koi ( Cyprinus carpio ) with Immunocytochemistry Test Streptavidin Biotin

Wahyuningtyas

Yanuhar

2018

RJLS

View full text Add to dashboard Cite

Koi herpesvirus (KHV) has been identified in common carp (Cyprinus carpio) and varieties of C. carpio such as koi carp. Handling KHV outbreak on koi fish are always late and on case KHV infection, hence the purpose of this study is to find an alternative method in identifying a particular fish diseases KHV which more simple, practical and accurate. 20 samples are positively infected by KHV were derived from Blitar, with the characteristic of them are gill slime, erosion or ulcers on the skin, movement were not controlled, and skin blister. The result of our study showed that 100% positive reaction to the ICC in smear blood, which is marked golden chocolate color. The result of immunostaining streptavidin biotin obtained that koi fish have been infected by severe KHV showed golden chocolate color on the blood smear compared to positive control. While fish have been infected by undemanding KHV infection or still in the beginning stage, the blood smear showed chocolate bluish. It can be concluded that Immunocytochemistry Test Streptavidin Biotin can be used for early identifying of Koi Herpes Virus (KHV) due to simpler producer, more practical, and accurate result.

show abstract

Discovery of Viruses and Virus-Like Pathogens in Pistachio using High-Throughput Sequencing

Cited by 52 publications

References 18 publications

The Detection and Surveillance of Asian Citrus Psyllid (Diaphorina citri)—Associated Viruses in Florida Citrus Groves

The Detection and Surveillance of Asian Citrus Psyllid (Diaphorina citri)—Associated Viruses in Florida Citrus Groves

Grapevine virus L: a Novel Vitivirus in Grapevine

Identification of Koi Herpesvirus on Fish Koi ( Cyprinus carpio ) with Immunocytochemistry Test Streptavidin Biotin

Contact Info

Product

Resources

About