Detect PNP: Detecting plant nursery pathogens using high throughput sequencing technology

Fully funded 4 year PhD available at Trinity College Dublin                                          

  “Detect PNP: Detecting plant nursery pathogens using HTS technology”

The project aims to provide methods for the detection of pathogens in plant nurseries using high- throughput DNA sequencing (HTS) technologies. Plant nurseries are normally inspected visually for pathogen collection and screening however this is time consuming and relies on the presence of the disease symptoms and the specialist knowledge of the inspector. To overcome these limitations, HTS methods offer high potential through eDNA application for pathogen detection and quantification. We will sample wastewater, growing media and plant material from nursery, botanic garden and research environments and develop the HTS pipelines for long and short read sequence detection of pathogens. It will also use whole genome sequencing of core isolated and cultured target microbes to provide genomic reference tools for further characterisation and screening. The focus is on hardy ornamental nursery stock and fungal and bacterial non-quarantine pathogens of Rhododendron and Prunus including Phytopthora and Pseudomonas but this project will provide a more general methodology to apply these methods in routine pathogen surveillance, to guide inspection staff, and to understand the implications of this approach for the detection and regulation of plant pathogens. The project will develop a road map on how the HTS technology could be used to augment plant health surveillance in nurseries and other ecosystems in Ireland. It is a collaboration between Trinity College Dublin, Teagasc, DAFM and the National Botanic Gardens Glasnevin.

This scholarship includes:

·       EU Fees for a PhD in Science at TCD for 4 years

·       An additional stipend: €25,000 annually (for 4 years)

You must be able to work independently, be hard working and solution-oriented and willing to participate fully within a dynamic and friendly research team. The successful candidate will hold an Honours Degree (2.1 or higher) in a cognate discipline (e.g. Botany, Plant Sciences, Agriculture, Genetics). An MSc or equivalent research experience would be an advantage. Other highly desirable skills include previous experience of lab-based molecular techniques, data analyses (e.g. experimental design, bioinformatics), and a demonstrated ability to communicate research findings.

Applications should comprise of a single PDF Document that contains the following:

A cover letter: Your letter should clearly set out your suitability and motivation for this PhD with reference to your past relevant experience and achievements.

A CV that includes your relevant experience, undergraduate results, postgraduate results (if applicable), any relevant publications and contact information for 2 academic referees.

Please send applications by 8^th of August 2024 to: Trevor.Hodkinson@tcd.ie

This project is funded by the Department of Agriculture, Food and the Marine (DAFM) Research Stimulus Fund.