scholarly journals Application of Oxford Nanopore Technology to Plant Virus Detection

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1424
Author(s):  
Lia W. Liefting ◽  
David W. Waite ◽  
Jeremy R. Thompson
Keyword(s):  
Plant Virus ◽  
High Throughput Sequencing ◽  
Virus Detection ◽  
Diagnostic Methods ◽  
Plant Virus Detection ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Virus Diagnostics ◽  
Post Entry ◽  
Read Accuracy

The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The portability of the MinION and Flongle platforms combined with lowering costs and continued improvements in read accuracy make ONT an attractive method for both low- and high-scale virus diagnostics. Here, we provide a detailed step-by-step protocol using the ONT Flongle platform that we have developed for the routine application on a range of symptomatic post-entry quarantine and domestic surveillance plant samples. The aim of this methods paper is to highlight ONT’s feasibility as a valuable component to the diagnostician’s toolkit and to hopefully stimulate other laboratories towards the eventual goal of integrating high-throughput sequencing technologies as validated plant virus diagnostic methods in their own right.

scholarly journals High Throughput Sequencing For Plant Virus Detection and Discovery

2019 ◽  
Vol 109 (5) ◽  
pp. 716-725 ◽  
Author(s):  
D. E. V. Villamor ◽  
T. Ho ◽  
M. Al Rwahnih ◽  
R. R. Martin ◽  
I. E. Tzanetakis
Keyword(s):  
High Throughput ◽  
Plant Virus ◽  
High Throughput Sequencing ◽  
Virus Detection ◽  
Agricultural Crops ◽  
Virus Discovery ◽  
Plant Virus Detection ◽  
Virus Biology ◽  
Disease Causality

Over the last decade, virologists have discovered an unprecedented number of viruses using high throughput sequencing (HTS), which led to the advancement of our knowledge on the diversity of viruses in nature, particularly unraveling the virome of many agricultural crops. However, these new virus discoveries have often widened the gaps in our understanding of virus biology; the forefront of which is the actual role of a new virus in disease, if any. Yet, when used critically in etiological studies, HTS is a powerful tool to establish disease causality between the virus and its host. Conversely, with globalization, movement of plant material is increasingly more common and often a point of dispute between countries. HTS could potentially resolve these issues given its capacity to detect and discover. Although many pipelines are available for plant virus discovery, all share a common backbone. A description of the process of plant virus detection and discovery from HTS data are presented, providing a summary of the different pipelines available for scientists’ utility in their research.

scholarly journals Application of image recognition for plant virus detection

2021 ◽  
Vol 27 (S1) ◽  
pp. 2274-2276
Author(s):  
Min-Sheng Hung ◽  
Yi-Tzu Chiu
Keyword(s):  
Image Recognition ◽  
Plant Virus ◽  
Virus Detection ◽  
Plant Virus Detection

scholarly journals Improving the Chromosome-Level Genome Assembly of the Siamese Fighting Fish (Betta splendens) in a University Master’s Course

2020 ◽  
Vol 10 (7) ◽  
pp. 2179-2183 ◽  
Author(s):  
Stefan Prost ◽  
Malte Petersen ◽  
Martin Grethlein ◽  
Sarah Joy Hahn ◽  
Nina Kuschik-Maczollek ◽  
...  
Keyword(s):  
Genome Assembly ◽  
High Throughput Sequencing ◽  
Siamese Fighting Fish ◽  
Betta Splendens ◽  
High Quality ◽  
Sequencing Platform ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read ◽  
Chromosome Level

Ever decreasing costs along with advances in sequencing and library preparation technologies enable even small research groups to generate chromosome-level assemblies today. Here we report the generation of an improved chromosome-level assembly for the Siamese fighting fish (Betta splendens) that was carried out during a practical university master’s course. The Siamese fighting fish is a popular aquarium fish and an emerging model species for research on aggressive behavior. We updated the current genome assembly by generating a new long-read nanopore-based assembly with subsequent scaffolding to chromosome-level using previously published Hi-C data. The use of ∼35x nanopore-based long-read data sequenced on a MinION platform (Oxford Nanopore Technologies) allowed us to generate a baseline assembly of only 1,276 contigs with a contig N50 of 2.1 Mbp, and a total length of 441 Mbp. Scaffolding using the Hi-C data resulted in 109 scaffolds with a scaffold N50 of 20.7 Mbp. More than 99% of the assembly is comprised in 21 scaffolds. The assembly showed the presence of 96.1% complete BUSCO genes from the Actinopterygii dataset indicating a high quality of the assembly. We present an improved full chromosome-level assembly of the Siamese fighting fish generated during a university master’s course. The use of ∼35× long-read nanopore data drastically improved the baseline assembly in terms of continuity. We show that relatively in-expensive high-throughput sequencing technologies such as the long-read MinION sequencing platform can be used in educational settings allowing the students to gain practical skills in modern genomics and generate high quality results that benefit downstream research projects.

scholarly journals Current impact and future directions of high throughput sequencing in plant virus diagnostics

2014 ◽  
Vol 188 ◽  
pp. 90-96 ◽  
Author(s):  
Sebastien Massart ◽  
Antonio Olmos ◽  
Haissam Jijakli ◽  
Thierry Candresse
Keyword(s):  
High Throughput ◽  
Plant Virus ◽  
High Throughput Sequencing ◽  
Future Directions ◽  
Virus Diagnostics ◽  
Current Impact

Recombinase polymerase amplification applied to plant virus detection and potential implications

2018 ◽  
Vol 546 ◽  
pp. 72-77 ◽  
Author(s):  
Binoy Babu ◽  
Francisco M. Ochoa-Corona ◽  
Mathews L. Paret
Keyword(s):  
Plant Virus ◽  
Virus Detection ◽  
Recombinase Polymerase Amplification ◽  
Plant Virus Detection

Simple method for plant virus detection: effect of antibody immobilization technique

2002 ◽  
Vol 105 (1) ◽  
pp. 141-146 ◽  
Author(s):  
P.M Boltovets ◽  
V.R Boyko ◽  
I.Yu Kostikov ◽  
N.S Dyachenko ◽  
B.A Snopok ◽  
...  
Keyword(s):  
Plant Virus ◽  
Virus Detection ◽  
Antibody Immobilization ◽  
Simple Method ◽  
Plant Virus Detection ◽  
Detection Effect

scholarly journals Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics

2021 ◽  
Author(s):  
Vahid Jalali Javaran ◽  
Peter Moffett ◽  
Pierre Lemoyne ◽  
Dong Xu ◽  
Charith-Raj Adkar Purushothama ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Virus Detection ◽  
Diagnostic Methods ◽  
Wine Industry ◽  
Vitis Vinifera L ◽  
Nanopore Sequencing ◽  
Third Generation ◽  
Third Generation Sequencing ◽  
The World ◽  
Generation Sequencing

Among all economically important plant species in the world, grapevine (Vitis vinifera L.) is the most cultivated fruit plant. It has a significant impact on the economies of many countries through wine and fresh and dried fruit production. In recent years, the grape and wine industry has been facing outbreaks of known and emerging viral diseases across the world. Although high-throughput sequencing (HTS) has been used extensively in grapevine virology, the application and potential of third-generation sequencing have not been explored in understanding grapevine viruses and their impact on the grapevine. Nanopore sequencing, a third-generation technology, can be used for direct sequencing of both RNA and DNA with minimal infrastructure. Compared to other HTS methods, the MinION nanopore platform is faster and more cost-effective and allows for long-read sequencing. Due to the size of the MinION device, it can be easily carried for field viral disease surveillance. This review article discusses grapevine viruses and their diagnostic methods, the principle of nanopore sequencing technology and its application in grapevine virus detection, virus–plant interactions, as well as the characterization of viral RNA modifications.

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