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

Plant Disease ◽  
2018 ◽  
Vol 102 (7) ◽  
pp. 1419-1425 ◽  
Author(s):  
Maher Al Rwahnih ◽  
Adib Rowhani ◽  
Nathaniel Westrick ◽  
Kristian Stevens ◽  
Alfredo Diaz-Lara ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Amino Acid Sequence Identity ◽  
Sequence Similarity ◽  
Sequence Information ◽  
Virus Species ◽  
Significant Sequence Similarity ◽  
Novel Virus ◽  
Polymerase Chain ◽  
Multiple Samples

Pistachio (Pistacia vera L.) trees from the National Clonal Germplasm Repository (NCGR) and orchards in California were surveyed for viruses and virus-like agents by high-throughput sequencing (HTS). Analyses of sequence information from 60 trees identified a novel virus, provisionally named “Pistachio ampelovirus A” (PAVA), in the NCGR that showed low amino acid sequence identity (approximately 42%) compared with members of the genus Ampelovirus (family Closteroviridae). A putative viroid, provisionally named “Citrus bark cracking viroid-pistachio” (CBCVd-pis), was also found in the NCGR and showed approximately 87% similarity to Citrus bark cracking viroid (CBCVd, genus Cocadviroid, family Pospiviroidae). Both PAVA and CBCVd-pis were graft transmissible to healthy UCB-1 hybrid rootstock seedlings (P. atlantica × P. integerrima). A field survey of 123 trees from commercial orchards found no incidence of PAVA but five (4%) samples were infected with CBCVd-pis. Of 675 NCGR trees, 16 (2.3%) were positive for PAVA and 172 (25.4%) were positive for CBCVd-pis by reverse-transcription polymerase chain reaction. Additionally, several contigs across multiple samples exhibited significant sequence similarity to a number of other plant virus species in different families. These findings require further study and confirmation. This study establishes the occurrence of viral and viroid populations infecting pistachio trees.

scholarly journals High-Throughput Sequencing Facilitates Discovery of New Plant Viruses in Poland

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 820
Author(s):  
Julia Minicka ◽  
Aleksandra Zarzyńska-Nowak ◽  
Daria Budzyńska ◽  
Natasza Borodynko-Filas ◽  
Beata Hasiów-Jaroszewska
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Plant Viruses ◽  
Yellow Mosaic Virus ◽  
Virus Species ◽  
Phylogenetic Groups ◽  
Accurate Identification ◽  
Detection And Identification ◽  
New Finding ◽  
Recent Occurrence

Viruses cause epidemics on all major crops of agronomic importance, and a timely and accurate identification is essential for control. High throughput sequencing (HTS) is a technology that allows the identification of all viruses without prior knowledge on the targeted pathogens. In this paper, we used HTS technique for the detection and identification of different viral species occurring in single and mixed infections in plants in Poland. We analysed various host plants representing different families. Within the 20 tested samples, we identified a total of 13 different virus species, including those whose presence has not been reported in Poland before: clover yellow mosaic virus (ClYMV) and melandrium yellow fleck virus (MYFV). Due to this new finding, the obtained sequences were compared with others retrieved from GenBank. In addition, cucurbit aphid-borne yellows virus (CABYV) was also detected, and due to the recent occurrence of this virus in Poland, a phylogenetic analysis of these new isolates was performed. The analysis revealed that CABYV population is highly diverse and the Polish isolates of CABYV belong to two different phylogenetic groups. Our results showed that HTS-based technology is a valuable diagnostic tool for the identification of different virus species originating from variable hosts, and can provide rapid information about the spectrum of plant viruses previously not detected in a region.

scholarly journals MultiGeMS: detection of SNVs from multiple samples using model selection on high-throughput sequencing data

2016 ◽  
Vol 32 (10) ◽  
pp. 1486-1492 ◽  
Author(s):  
Gabriel H. Murillo ◽  
Na You ◽  
Xiaoquan Su ◽  
Wei Cui ◽  
Muredach P. Reilly ◽  
...  
Keyword(s):  
Model Selection ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequencing Data ◽  
High Throughput Sequencing Data ◽  
Multiple Samples

scholarly journals Characterization of Ti Ringspot-Associated Virus, a Novel Emaravirus Associated with an Emerging Ringspot Disease of Cordyline fruticosa

Plant Disease ◽  
2019 ◽  
Vol 103 (9) ◽  
pp. 2345-2352 ◽  
Author(s):  
Alejandro Olmedo-Velarde ◽  
Adam C. Park ◽  
Jari Sugano ◽  
Janice Y. Uchida ◽  
Michael Kawate ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
High Plains ◽  
Virus Species ◽  
Sequence Analyses ◽  
Sequence Identity ◽  
Reverse Transcription Pcr ◽  
Eriophyid Mites ◽  
Cordyline Fruticosa ◽  
Novel Virus

Ti ringspot is an emerging foliar disease of the ti plant (Cordyline fruticosa) in Hawaii that is quickly spreading throughout the islands. Symptoms include small chlorotic ringspots on leaves that often coalesce to form larger lesions. Although several virus species have been discovered in symptomatic plants, none have been associated with these symptoms. Here, we report and characterize a novel virus closely associated with ti ringspot symptoms in Hawaii. The presence of double membrane bodies approximately 85 nm in diameter in symptomatic cells and sequence analyses of five genomic RNA segments obtained by high-throughput sequencing indicate that this virus is most closely related to members of the plant virus genus Emaravirus. Phylogenetic and sequence homology analyses place this virus on a distinct clade within the Emaravirus genus along with High Plains wheat mosaic emaravirus, blue palo verde broom virus, and Raspberry leaf blotch emaravirus. Sequence identity values with taxonomically relevant proteins indicate that this represents a new virus species, which we are tentatively naming ti ringspot-associated virus (TiRSaV). TiRSaV-specific reverse transcription PCR assays detected the virus in several experimental herbaceous host species following mechanical inoculation. TiRSaV was also detected in eriophyid mites collected from symptomatic ti plants, which may represent a putative arthropod vector of the virus.

scholarly journals Double-Stranded RNA High-Throughput Sequencing Reveals a New Cytorhabdovirus in a Bean Golden Mosaic Virus-Resistant Common Bean Transgenic Line

Viruses ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 90 ◽  
Author(s):  
Dione M. T. Alves-Freitas ◽  
Bruna Pinheiro-Lima ◽  
Josias C. Faria ◽  
Cristiano Lacorte ◽  
Simone G. Ribeiro ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Mosaic Virus ◽  
High Throughput ◽  
Transgenic Line ◽  
High Throughput Sequencing ◽  
Open Reading Frames ◽  
Virus Species ◽  
Homologous Proteins ◽  
Bean Golden Mosaic Virus

Using double-strand RNA (dsRNA) high-throughput sequencing, we identified five RNA viruses in a bean golden mosaic virus (BGMV)-resistant common bean transgenic line with symptoms of viral infection. Four of the identified viruses had already been described as infecting common bean (cowpea mild mottle virus, bean rugose mosaic virus, Phaseolus vulgaris alphaendornavirus 1, and Phaseolus vulgaris alphaendornavirus 2) and one is a putative new plant rhabdovirus (genus Cytorhabdovirus), tentatively named bean-associated cytorhabdovirus (BaCV). The BaCV genome presented all five open reading frames (ORFs) found in most rhabdoviruses: nucleoprotein (N) (ORF1) (451 amino acids, aa), phosphoprotein (P) (ORF2) (445 aa), matrix (M) (ORF4) (287 aa), glycoprotein (G) (ORF5) (520 aa), and an RNA-dependent RNA polymerase (L) (ORF6) (114 aa), as well as a putative movement protein (P3) (ORF3) (189 aa) and the hypothetical small protein P4. The predicted BaCV proteins were compared to homologous proteins from the closest cytorhabdoviruses, and a low level of sequence identity (15–39%) was observed. The phylogenetic analysis shows that BaCV clustered with yerba mate chlorosis-associated virus (YmCaV) and rice stripe mosaic virus (RSMV). Overall, our results provide strong evidence that BaCV is indeed a new virus species in the genus Cytorhabdovirus (family Rhabdoviridae), the first rhabdovirus to be identified infecting common bean.

scholarly journals Quality Assessment and Validation of High-Throughput Sequencing for Grapevine Virus Diagnostics

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1130
Author(s):  
Nourolah Soltani ◽  
Kristian A. Stevens ◽  
Vicki Klaassen ◽  
Min-Sook Hwang ◽  
Deborah A. Golino ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Plant Viruses ◽  
Molecular Diagnostic ◽  
Virus Species ◽  
Certification Programs ◽  
Performance Specifications ◽  
Virus Diagnostics ◽  
Diagnostic Research ◽  
And Performance

Development of High-Throughput Sequencing (HTS), also known as next generation sequencing, revolutionized diagnostic research of plant viruses. HTS outperforms bioassays and molecular diagnostic assays that are used to screen domestic and quarantine grapevine materials in data throughput, cost, scalability, and detection of novel and highly variant virus species. However, before HTS-based assays can be routinely used for plant virus diagnostics, performance specifications need to be developed and assessed. In this study, we selected 18 virus-infected grapevines as a test panel for measuring performance characteristics of an HTS-based diagnostic assay. Total nucleic acid (TNA) was extracted from petioles and dormant canes of individual samples and constructed libraries were run on Illumina NextSeq 500 instrument using a 75-bp single-end read platform. Sensitivity was 98% measured over 264 distinct virus and viroid infections with a false discovery rate (FDR) of approximately 1 in 5 positives. The results also showed that combining a spring petiole test with a fall cane test increased sensitivity to 100% for this TNA HTS assay. To evaluate extraction methodology, these results were compared to parallel dsRNA extractions. In addition, in a more detailed dilution study, the TNA HTS assay described here consistently performed well down to a dilution of 5%. In that range, sensitivity was 98% with a corresponding FDR of approximately 1 in 5. Repeatability and reproducibility were assessed at 99% and 93%, respectively. The protocol, criteria, and performance levels described here may help to standardize HTS for quality assurance and accreditation purposes in plant quarantine or certification programs.

Analysis of the bacterial communities in the waterlogged wooden cultural relics of the Xiaobaijiao No. 1 shipwreck via high-throughput sequencing technology

Holzforschung ◽  
2018 ◽  
Vol 72 (7) ◽  
pp. 609-619 ◽  
Author(s):  
Qiuxia Li ◽  
Lixiang Cao ◽  
Wenfeng Wang ◽  
Hongming Tan ◽  
Tao Jin ◽  
...  
Keyword(s):  
High Throughput ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Diversity Index ◽  
Sequence Similarity ◽  
Species Number ◽  
Sequencing Technology ◽  
Α Diversity ◽  
Sea Area ◽  
Cultural Relics

AbstractThe microbial impact on waterlogged wooden cultural relics fromXiaobaijiao No. 1shipwreck was investigated by means of a high-throughput sequencing technology, while the focus was on the composition of prokaryotic microorganisms in 10 wood samples collected from different parts of the shipwreck. A total of 28 501 different operational taxonomic units (OTUs) were obtained based on 97% sequence similarity. The α-diversity index is for the bacterial diversity, which was the highest and the lowest in the samples SS8 and SS5, respectively. Proteobacteria was the largest category of bacterial abundance (47.3%) followed by Bacteroidetes (10%). α-Proteobacteria was the first largest bacteria class with the maximum abundance (21.0%) followed by γ-Proteobacteria (16.9%). Other groups rich in the following species were found: Bacteroidales (13.3%), Thiotrichales (5.0%), Rhodobacterales (4.2%), Rhizobiales (4.0%), Chromatiales (3.5%), Oceanospirillales (3.3%), Flavobacteriales (2.9%) and Sphingomonadales (2.8%). At the level of the bacterial genus,Marinomonaswas the most abundant one. Phylogenetic analysis revealed that there are some differences in the composition of bacterial communities from different wood samples. The species number of bacteria in the relics of this shipwreck was far more than that reported in those found in Europe, and in which species composition was similar to the benthic bacteria in the corresponding sea area. The coexistence of anaerobic and aerobic bacteria is remarkable.

scholarly journals The Diversity and Distribution of Viruses Associated with Culex annulirostris Mosquitoes from the Kimberley Region of Western Australia

Viruses ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 717 ◽  
Author(s):  
Simon H. Williams ◽  
Avram Levy ◽  
Rachel A. Yates ◽  
Nilusha Somaweera ◽  
Peter J. Neville ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
High Throughput ◽  
Western Australia ◽  
High Throughput Sequencing ◽  
Marked Variation ◽  
Chain Reaction ◽  
Virus Prevalence ◽  
Culex Annulirostris ◽  
Polymerase Chain ◽  
Viral Sequences

Metagenomics revealed an impressive breadth of previously unrecognized viruses. Here, we report the virome of the Culex annulirostris Skuse mosquito, an important vector of pathogenic arboviruses in Australia. Mosquitoes were collected from three sites in the Kimberley region of Western Australia. Unbiased high-throughput sequencing (HTS) revealed the presence of 16 novel viral sequences that share less than 90% identity with known viruses. None were closely related to pathogenic arboviruses. Viruses were distributed unevenly across sites, indicating a heterogeneous Cx. annulirostris virome. Polymerase chain reaction assays confirmed HTS data and identified marked variation between the virus prevalence identified at each site.

scholarly journals Identification of conserved hepatic transcriptomic responses to 17β-estradiol using high-throughput sequencing in brown trout

2015 ◽  
Vol 47 (9) ◽  
pp. 420-431 ◽  
Author(s):  
Tamsyn M. Uren Webster ◽  
Janice A. Shears ◽  
Karen Moore ◽  
Eduarda M. Santos
Keyword(s):  
High Throughput ◽  
Brown Trout ◽  
Ribosome Biogenesis ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Cellular Proliferation ◽  
Sequence Information ◽  
Rna Seq ◽  
Mechanisms Of Toxicity ◽  
17Β Estradiol

Estrogenic chemicals are major contaminants of surface waters and can threaten the sustainability of natural fish populations. Characterization of the global molecular mechanisms of toxicity of environmental contaminants has been conducted primarily in model species rather than species with limited existing transcriptomic or genomic sequence information. We aimed to investigate the global mechanisms of toxicity of an endocrine disrupting chemical of environmental concern [17β-estradiol (E2)] using high-throughput RNA sequencing (RNA-Seq) in an environmentally relevant species, brown trout ( Salmo trutta). We exposed mature males to measured concentrations of 1.94, 18.06, and 34.38 ng E2/l for 4 days and sequenced three individual liver samples per treatment using an Illumina HiSeq 2500 platform. Exposure to 34.4 ng E2/L resulted in 2,113 differentially regulated transcripts (FDR < 0.05). Functional analysis revealed upregulation of processes associated with vitellogenesis, including lipid metabolism, cellular proliferation, and ribosome biogenesis, together with a downregulation of carbohydrate metabolism. Using real-time quantitative PCR, we validated the expression of eight target genes and identified significant differences in the regulation of several known estrogen-responsive transcripts in fish exposed to the lower treatment concentrations (including esr1 and zp2.5). We successfully used RNA-Seq to identify highly conserved responses to estrogen and also identified some estrogen-responsive transcripts that have been less well characterized, including nots and tgm2l. These results demonstrate the potential application of RNA-Seq as a valuable tool for assessing mechanistic effects of pollutants in ecologically relevant species for which little genomic information is available.

scholarly journals Use of High-Throughput Sequencing and Two RNA Input Methods to Identify Viruses Infecting Tomato Crops

2021 ◽  
Vol 9 (5) ◽  
pp. 1043
Author(s):  
Ayoub Maachi ◽  
Covadonga Torre ◽  
Raquel N. Sempere ◽  
Yolanda Hernando ◽  
Miguel A. Aranda ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Tomato Fruit ◽  
Virus Detection ◽  
Read Depth ◽  
Cdna Libraries ◽  
Virus Species ◽  
Total Rna ◽  
Viral Genomes ◽  
First Time

We used high-throughput sequencing to identify viruses on tomato samples showing virus-like symptoms. Samples were collected from crops in the Iberian Peninsula. Either total RNA or double-stranded RNA (dsRNA) were used as starting material to build the cDNA libraries. In total, seven virus species were identified, with pepino mosaic virus being the most abundant one. The dsRNA input provided better coverage and read depth but missed one virus species compared with the total RNA input. By performing in silico analyses, we determined a minimum sequencing depth per sample of 0.2 and 1.5 million reads for dsRNA and rRNA-depleted total RNA inputs, respectively, to detect even the less abundant viruses. Primers and TaqMan probes targeting conserved regions in the viral genomes were designed and/or used for virus detection; all viruses were detected by qRT-PCR/RT-PCR in individual samples, with all except one sample showing mixed infections. Three virus species (Olive latent virus 1, Lettuce ring necrosis virus and Tomato fruit blotch virus) are herein reported for the first time in tomato crops in Spain.

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