Projects / Programmes
Nanopore high-throughput sequencing for resolution of problems in plant pathogen epidemiology and diagnostics
| Code |
Science |
Field |
Subfield |
| 4.06.05 |
Biotechnical sciences |
Biotechnology |
Plant biotechnology |
| 4.03.01 |
Biotechnical sciences |
Plant production |
Agricultural plants |
| Code |
Science |
Field |
| 4.04 |
Agricultural and Veterinary Sciences |
Agricultural biotechnology |
| 4.01 |
Agricultural and Veterinary Sciences |
Agriculture, Forestry and Fisheries |
Plant virus, phytoplasma, high throughput sequencing, nanopore, viroid
Data for the last 5 years (citations for the last 10 years) on
June 25, 2024;
A3 for period
2018-2022
Data for ARIS tenders (
04.04.2019 – Programme tender,
archive
)
| Database |
Linked records |
Citations |
Pure citations |
Average pure citations |
| WoS |
425 |
15,868 |
14,184 |
33.37 |
| Scopus |
451 |
17,475 |
15,630 |
34.66 |
Researchers (17)
Organisations (3)
Abstract
High-throughput sequencing (HTS) has revolutionized microbial research as it is the only generic, non-targeted molecular method for discovery of unknown and known microbes, including emerging pathogens in human, animal, plant and environmental samples (such as water and soil). One of the limitations, which restrict the widespread use of currently commonly used HTS platforms (e.g., Illumina), is that it generally requires expensive sequencers or few weeks’ time if samples are sent to external sequencing providers. Nanopore-based sequencing technology (i.e., Oxford Nanopore Technologies) is rapidly developing in past few years and shows a great potential for economical use of HTS in laboratories of different sizes (very small to very big), both in terms of time and money. It is also currently the only HTS approach, which shows potential for analysis of samples outside laboratories. In addition, in contrary to most of the other commonly used HTS platforms, nanopore allows sequencing of long genome fragments, such as complete viral genomes, and therefore offers possibility for more effective differentiation between genotypes of the same microbe species, when they are present, e.g., in complex mixtures. In this project, we will explore the nanopore sequencing as a complement and/or substitute to short reads sequencing (Illumina) method for discovery of pathogenic microbes in plants and for resolving important epidemiological issues. Our preliminary research suggests that the method could be useful for determining all types of virus genomes including viroids. We aim to demonstrate this through a comprehensive comparative study by sequencing total RNA from infected plant samples using Illumina and nanopore sequencing approaches. Next, we will apply nanopore sequencing for the study of virus-infected plants e.g. tomatoes, and test its performance especially for construction of complete viral genomes in the case of mixed infections with multiple viral genotypes. The research will be directed also towards preparation of nanopore technology for rapid and affordable virus detection in the field and water samples. Furthermore, we will employ nanopore sequencing in combination with Illumina to address epidemiological problems in plant pathology. As an example study, we will use recently discovered Flavescence dorée (FD)-related phytoplasmas in hazelnuts (Corylus avellana), identified only based on partial 16S rRNA, secY, map and ribosomal protein genetic locus. Further studies are needed to investigate the hazelnuts and grapevines phytoplasmas, aiming to obtain as much information as possible about their genome, since it is not available in complete information and to reveal the relation of both phytoplasmas. If the equality of both genomes will be confirmed, it will radically change the epidemiology and measures of plant protection against FD phytoplasma that is quarantine pathogen. If not, we will revise FD determination methods and develop tests that distinguish between both and other non-quarantine species of grapevine yellows phytoplasmas. With upgrading the results of two described working packages related to virus discovery and epidemiology, we will develop high-throughput sequencing for simultaneous detection of different types of microbes in a single sample. We will isolate and sequence total RNA from plants (e.g. grapevine) infected with viruses and phytoplasmas. In the project, we will use state-of-the-art bioinformatic tools and develop new algorithms and workflows for data processing and interpretation. Experienced interdisciplinary research team will assure project success in addressing global trend of developing HTS and specifically nanopore technology to develop new approaches in epidemiology, microbial discovery and diagnostics. This will lead to better plant protection, which is indispensable in catching up with the rapid spread of pathogens because of climate change and rapid movement of plants and plant products.
