Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing

This paper describes the application of next generation sequencing (NGS) in plant virus research. Although NGS has not been routinely used yet, it is increasingly adopted in diagnostics and genomics of phytopathogens. NGS technics enable the simultaneous detection of multiple viruses present in infected material. This makes it possible not only to determine which viruses are present in a single sample but also to determine their concentration and genetic diversity. The simultaneous identification of many viruses, the possibility of early detection of disease outbreaks as well as tracking and monitoring of epidemic development, make NGS a universal research tool that enables not only the detection but also the understanding of molecular mechanisms allowing viruses to adapt to environmental changes (host plant genotype, vector, presence of other pathogens).

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Diagnosis of Plant Viruses Using Next-Generation Sequencing and Metagenomic Analysis

Current Research Topics in Plant Virology ◽

10.1007/978-3-319-32919-2_14 ◽

2016 ◽

pp. 323-335 ◽

Cited By ~ 8

Author(s):

Ian Adams ◽

Adrian Fox

Keyword(s):

Next Generation Sequencing ◽

Plant Viruses ◽

Metagenomic Analysis ◽

Next Generation ◽

Generation Sequencing

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Next-Generation Sequencing and the CRISPR-Cas Nexus: A Molecular Plant Virology Perspective

Frontiers in Microbiology ◽

10.3389/fmicb.2020.609376 ◽

2021 ◽

Vol 11 ◽

Author(s):

Muhammad Shafiq Shahid ◽

Muhammad Naeem Sattar ◽

Zafar Iqbal ◽

Amir Raza ◽

Abdullah M. Al-Sadi

Keyword(s):

Next Generation Sequencing ◽

Plant Viruses ◽

Genetically Engineered ◽

Site Directed Mutagenesis ◽

Host Susceptibility ◽

Base Substitution ◽

Next Generation ◽

Plant Virology ◽

Detection Techniques ◽

Generation Sequencing

In recent years, next-generation sequencing (NGS) and contemporary Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) technologies have revolutionized the life sciences and the field of plant virology. Both these technologies offer an unparalleled platform for sequencing and deciphering viral metagenomes promptly. Over the past two decades, NGS technologies have improved enormously and have impacted plant virology. NGS has enabled the detection of plant viruses that were previously undetectable by conventional approaches, such as quarantine and archeological plant samples, and has helped to track the evolutionary footprints of viral pathogens. The CRISPR-Cas-based genome editing (GE) and detection techniques have enabled the development of effective approaches to virus resistance. Different versions of CRISPR-Cas have been employed to successfully confer resistance against diverse plant viruses by directly targeting the virus genome or indirectly editing certain host susceptibility factors. Applications of CRISPR-Cas systems include targeted insertion and/or deletion, site-directed mutagenesis, induction/expression/repression of the gene(s), epigenome re-modeling, and SNPs detection. The CRISPR-Cas toolbox has been equipped with precision GE tools to engineer the target genome with and without double-stranded (ds) breaks or donor templates. This technique has also enabled the generation of transgene-free genetically engineered plants, DNA repair, base substitution, prime editing, detection of small molecules, and biosensing in plant virology. This review discusses the utilities, advantages, applications, bottlenecks of NGS, and CRISPR-Cas in plant virology.

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Application of Next Generation Sequencing for Diagnostic Testing of Tree Fruit Viruses and Viroids

Plant Disease ◽

10.1094/pdis-03-17-0306-re ◽

2017 ◽

Vol 101 (8) ◽

pp. 1489-1499 ◽

Cited By ~ 27

Author(s):

M. Rott ◽

Y. Xiang ◽

I. Boyes ◽

M. Belton ◽

H. Saeed ◽

...

Keyword(s):

Next Generation Sequencing ◽

Diagnostic Testing ◽

Virus Detection ◽

Plant Viruses ◽

Next Generation ◽

Viral Pathogens ◽

Plant Virus Detection ◽

Biological Indexing ◽

Tree Fruit ◽

Generation Sequencing

Conventional detection of viruses and virus-like diseases of plants is accomplished using a combination of molecular, serological, and biological indexing. These are the primary tools used by plant virologists to monitor and ensure trees are free of known viral pathogens. The biological indexing assay, or bioassay, is considered to be the “gold standard” as it is the only method of the three that can detect new, uncharacterized, or poorly characterized viral disease agents. Unfortunately, this method is also the most labor intensive and can take up to three years to complete. Next generation sequencing (NGS) is a technology with rapidly expanding possibilities including potential applications for the detection of plant viruses. In this study, comparisons are made between tree fruit testing by conventional and NGS methods, to demonstrate the efficacy of NGS. A comparison of 178 infected trees, many infected with several viral pathogens, demonstrated that conventional and NGS were equally capable of detecting known viruses and viroids. Comparable results were obtained for 170 of 178 of the specimens. Of the remaining eight specimens, some discrepancies were observed between viruses detected by the two methods, representing less than 5% of the specimens. NGS was further demonstrated to be equal or superior for the detection of new or poorly characterized viruses when compared with a conventional bioassay. These results validated both the effectiveness of conventional virus testing methods and the use of NGS as an additional or alternative method for plant virus detection.

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