The impact of high throughput sequencing on plant health diagnostics

Adams, Ian; Fox, Adrian; Boonham, Neil; Massart, Sébastien; Jonghe, Kris De

doi:10.1007/s10658-018-1570-0

Cited by 58 publications

(51 citation statements)

References 69 publications

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“…It has many advantages over serological and molecular detection methods that require specific antisera or prior knowledge of nucleotide sequences [19]. Metagenomic HTS has significantly influenced the diagnosis of known and unknown plant viruses as well as genome diversity and evolutionary investigations at different taxonomic levels [14][15][16][17][18][19][20][21][22][23][24][25][26]. Recent advances in HTS technology and improved bioinformatics pipelines have appreciably reduced sequencing costs and time.…”

Section: Introductionmentioning

confidence: 99%

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

Samarfard

McTaggart

Sharman³

et al. 2020

Pathogens

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Alfalfa plants in the field can display a range of virus-like symptoms, especially when grown over many years for seed production. Most known alfalfa viruses have RNA genomes, some of which can be detected using diagnostic assays, but many viruses of alfalfa are not well characterized. This study aims to identify the RNA and DNA virus complexes associated with alfalfa plants in Australia. To maximize the detection of RNA viruses, we purified double-stranded RNA (dsRNA) for high throughput sequencing and characterized the viromes of ten alfalfa samples that showed diverse virus-like symptoms. Using Illumina sequencing of tagged cDNA libraries from immune-captured dsRNA, we identified sequences of the single-stranded RNA viruses, alfalfa mosaic virus (AMV), bean leafroll virus, a new emaravirus tentatively named alfalfa ringspot-associated virus, and persistent dsRNA viruses belonging to the families Amalgaviridae and Partitiviridae. Furthermore, rolling circle amplification and restriction enzyme digestion revealed the complete genome of chickpea chlorosis Australia virus, a mastrevirus (family Geminiviridae) previously reported only from chickpea and French bean that was 97% identical to the chickpea isolate. The sequence data also enabled the assembly of the first complete genome (RNAs 1–3) of an Australian AMV isolate from alfalfa.

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Section: Introductionmentioning

confidence: 99%

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

Samarfard

McTaggart

Sharman³

et al. 2020

Pathogens

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“…Despite the growing body of evidence for its usefulness in the early detection and surveillance of potentially invasive forest pathogens [27][28][29], and its high sensitivity and capacity to deal with large numbers of samples in less time compared to traditional methods [30], HTS is generally underutilized as a tool in plant biosecurity [31][32][33][34][35].…”

Section: Introductionmentioning

confidence: 99%

Cryptic Risks to Forest Biosecurity Associated with the Global Movement of Commercial Seed

Cleary

Oskay

Doğmuş

et al. 2019

Forests

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The import and export of tree seed carries with it risks of inadvertent introduction of pests and pathogens to hitherto unaffected regions. Although trade in seed of specified trees is regulated, phytosanitary requirements for most tree species are minimal, even those related to the most important forest tree species in a given region. A better understanding of the microbiome associated with seed intended for commercial production or ornamental use, and their potential risk with the transport from the source origin of distributors, will help regulatory agencies implement measures to safeguard seed health and avoid trade-related spread of potentially harmful pathogens. In this study we used high-throughput sequencing to show that highly diverse fungal communities were associated with seed of 14 different Pinus species obtained from seed banks (seed orchards) and retail sources (online distributors) in North America and Europe. Fungal diversity differed among the 23 seedlots tested. Community composition did not relate to the species of Pinus nor the country of origin. Assigned potential functions based on sequence identity using FUNGuild provided an overall understanding of the likely life strategies of fungal operational taxonomic units (OTUs). Of those sequences classified to a trophic level, 453 were plant pathogens, with the Dothideomycetes having the highest prevalence. The most common plant pathogens included Sydowia polyspora, Lasiodiplodia theobromae, Diplodia intermedia and Diplodia sapinea that were detected from the majority of Pinus species. The evidence presented here illustrates an urgent need for plant protection authorities, practitioners and the general public to recognize the potential risk of introducing harmful pathogens through innocent transport of seed.

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“…The availability of scientific knowledge as such will enable plant health, policymakers and regulators to make correct decisions. Recommended literature on this topic includes Adams et al [ 143 ] and Massart et al [ 144 ].…”

Section: Discussionmentioning

confidence: 99%

High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later

Ibaba

Gubba

2020

Plants

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High-throughput sequencing (HTS) application in the field of plant virology started in 2009 and has proven very successful for virus discovery and detection of viruses already known. Plant virology is still a developing science in most of Africa; the number of HTS-related studies published in the scientific literature has been increasing over the years as a result of successful collaborations. Studies using HTS to identify plant-infecting viruses have been conducted in 20 African countries, of which Kenya, South Africa and Tanzania share the most published papers. At least 29 host plants, including various agricultural economically important crops, ornamentals and medicinal plants, have been used in viromics analyses and have resulted in the detection of previously known viruses and novel ones from almost any host. Knowing that the effectiveness of any management program requires knowledge on the types, distribution, incidence, and genetic of the virus-causing disease, integrating HTS and efficient bioinformatics tools in plant virology research projects conducted in Africa is a matter of the utmost importance towards achieving and maintaining sustainable food security.

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The impact of high throughput sequencing on plant health diagnostics

Cited by 58 publications

References 69 publications

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

Cryptic Risks to Forest Biosecurity Associated with the Global Movement of Commercial Seed

High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later

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