Illuminating an ecological blackbox: using high throughput sequencing to characterize the plant virome across scales

F Maclot, T Candresse, D Filloux… - Frontiers in …, 2020 - frontiersin.org
The ecology of plant viruses began to be explored at the end of the 19th century. Since then,
major advances have revealed mechanisms of virus-host-vector interactions in various …

Next-generation sequencing and genome editing in plant virology

A Hadidi, R Flores, T Candresse, M Barba - Frontiers in microbiology, 2016 - frontiersin.org
Next-generation sequencing (NGS) has been applied to plant virology since 2009. NGS
provides highly efficient, rapid, low cost DNA, or RNA high-throughput sequencing of the …

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

G Lear, I Dickie, J Banks, S Boyer, HL Buckley… - New Zealand Journal of …, 2018 - JSTOR
Advances in the sequencing of DNA extracted from media such as soil and water offer huge
opportunities for biodiversity monitoring and assessment, particularly where the collection or …

A primer on the analysis of high-throughput sequencing data for detection of plant viruses

D Kutnjak, L Tamisier, I Adams, N Boonham… - Microorganisms, 2021 - mdpi.com
High-throughput sequencing (HTS) technologies have become indispensable tools
assisting plant virus diagnostics and research thanks to their ability to detect any plant virus …

Comparative study on three viral enrichment approaches based on RNA extraction for plant virus/viroid detection using high-throughput sequencing

YZA Gaafar, H Ziebell - PLoS One, 2020 - journals.plos.org
High-throughput sequencing (HTS) has become increasingly popular as virus diagnostic
tool. It has been used to detect and identify plant viruses and viroids in different types of …

Discovering and sequencing new plant viral genomes by next‐generation sequencing: description of a practical pipeline

R Blawid, JMF Silva, T Nagata - Annals of Applied Biology, 2017 - Wiley Online Library
Small‐scale sequencing has improved substantially in recent decades, culminating in the
development of next‐generation sequencing (NGS) technologies. Modern NGS methods …

Deep sequencing for discovery and evolutionary analysis of plant viruses

MJ Roossinck - Virus research, 2017 - Elsevier
The advent of next generation sequencing (NGS), or deep sequencing, has allowed great
advances to be made in discovery, diagnostics, and evolutionary studies in plant viruses …

RNA viruses in aquatic ecosystems through the lens of ecological genomics and transcriptomics

S Kolundžija, DQ Cheng, FM Lauro - Viruses, 2022 - mdpi.com
Massive amounts of data from nucleic acid sequencing have changed our perspective about
diversity and dynamics of marine viral communities. Here, we summarize recent …

Effective mosquito and arbovirus surveillance using metabarcoding

J Batovska, SE Lynch, NOI Cogan… - Molecular ecology …, 2018 - Wiley Online Library
Effective vector and arbovirus surveillance requires timely and accurate screening
techniques that can be easily upscaled. Next‐generation sequencing (NGS) is a high …

The plant negative-sense RNA virosphere: virus discovery through new eyes

N Bejerman, H Debat, RG Dietzgen - Frontiers in Microbiology, 2020 - frontiersin.org
The use of high-throughput sequencing (HTS) for virus diagnostics, as well as the
importance of this technology as a valuable tool for discovery of novel viruses has been …