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Projects / Programmes source: ARIS

Nanopore high-throughput sequencing for resolution of problems in plant pathogen epidemiology and diagnostics

Research activity

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 
Keywords
Plant virus, phytoplasma, high throughput sequencing, nanopore, viroid
Evaluation (rules)
source: COBISS
Points
3,936.03
A''
752.48
A'
2,286.68
A1/2
2,886.51
CI10
13,195
CImax
1,407
h10
54
A1
14.44
A3
15.75
Data for the last 5 years (citations for the last 10 years) on April 21, 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 (16)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  50563  PhD Katarina Bačnik  Biotechnology  Researcher  2020 - 2024  132 
2.  23399  PhD Tomaž Curk  Computer science and informatics  Researcher  2020 - 2024  253 
3.  08280  PhD Marina Dermastia  Biology  Researcher  2020 - 2024  872 
4.  57364  Rok Gomišček  Computer science and informatics  Researcher  2022 - 2024 
5.  27827  PhD Jon Gutierrez Aguirre  Biotechnology  Researcher  2020 - 2024  363 
6.  35424  PhD Tomaž Hočevar  Computer science and informatics  Researcher  2020 - 2024  30 
7.  39610  MSc Tina Klepac  Biotechnology  Researcher  2020 - 2024 
8.  52584  Zala Kogej Zwitter  Biotechnology  Junior researcher  2020 - 2024  104 
9.  35384  PhD Denis Kutnjak  Biotechnology  Researcher  2020 - 2024  288 
10.  50210  Janja Matičič  Biotechnology  Researcher  2020 - 2021 
11.  23610  PhD Nataša Mehle  Biotechnology  Researcher  2020 - 2024  542 
12.  38081  PhD Anja Pecman  Biotechnology  Researcher  2020 - 2024  98 
13.  30090  PhD Nina Prezelj  Biology  Technical associate  2023 - 2024  61 
14.  05229  PhD Maja Ravnikar  Biotechnology  Head  2020 - 2024  1,369 
15.  19626  Rok Štravs  Biotechnology  Researcher  2020 - 2024  18 
16.  09864  PhD Magda Tušek Žnidarič  Biology  Technical associate  2020 - 2024  414 
Organisations (3)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0105  National Institute of Biology  Ljubljana  5055784  13,256 
2.  0158  BIA, Laboratory and process equipment company, Ltd.  Ljubljana  5327601  18 
3.  1539  University of Ljubljana, Faculty of Computer and Information Science  Ljubljana  1627023  16,239 
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.
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