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Chromosomal plasticity and horizontal gene transfer in plant pathogenic fungi

Primary Supervisor: Dr Megan McDonald, School of Biosciences

Secondary supervisor: Dr Graeme Kettles

PhD project title: Chromosomal plasticity and horizontal gene transfer in plant pathogenic fungi

University of Registration: University of Birmingham

Project outline:

A major limit to global food security is annual, preventable yield loss due to plant diseases. Conservative estimates suggest that diseases cause by fungal pathogens are responsible for annual yield losses up to 5-10% globally and widespread fungal disease epidemics are common in our modern monoculture based agricultural system. In order to protect crop plants, farmers rely on a combination chemical control (fungicides) and plant genetic resistance (plant immunity) to prevent disease epidemics. However, these control measures are often short-lived as fungal pathogens rapidly evolve resistance to fungicides or alter their own secreted proteins to evade plant immune recognition. To protect future crop yields it is imperative that we understand how fungal pathogens are able to rapidly evolve in response to chemicals or plant genetic resistance.

The current research program in the McDonald Lab focuses on high-throughput identification and characterisation of fungal virulence genes using all available genomic technologies. We focus on the identification of virulence genes from diverse fungal isolates collected from natural plant infections (see Project 1) or re-sequencing and phenotyping of mutant populations generated experimentally (see Project 2 and 3).

Project 1: Genome plasticity and transposon-mediated horizontal gene transfer between fungal wheat pathogens

Our recently published work on the wheat and barley pathogen Bipolaris sorokiniana, a severe wheat disease in Bangladesh, suggests that high rates of chromosomal plasticity exist in naturally infecting populations and that this plasticity contributes to the spread of important virulence genes both within and between species (McDonald, 2019). These pathogenicity genes can be translocated across chromosomes and horizontally transferred between different pathogen species. This project will characterise the extent and frequency of these rapid chromosomal rearrangements in three fungal wheat pathogens. This will involve whole-genome resequencing of a global collection of fungal isolates, followed by comprehensive genome and transposon annotation. This project will also characterise chromosomal plasticity using long-read whole genome sequencing coupled with 3D genome re-construction techniques (Hi-C).

Project 2: Forward genetics screening of genes controlling host-specificity and virulence

This project seeks to understand the molecular basis for host-specificity in the wheat and barley pathogen B. sorokiniana. This fungal pathogen is adept at infecting both of these important crops, causing wide-spread necrosis of leaf tissue. We currently have no understanding of the genes required for infection on either host. This project will utilise a forward genetics screen to identify mutants that lose the ability to infect either host. Whole-genome resequencing of a panel of mutants will be used to identify gene-candidates which will be further investigated using reverse genetics.

Project 3: Gene-editing approaches to identify gene essentiality in plant pathogenic fungi

The fungal wheat pathogen Zymoseptoria tritici is one of the most serious diseases of wheat in the UK. This pathogen is also the primary target of foliar applied fungicides, with an estimated cost in Europe of ~€1.2 bn. While fungicide application is essential to protect wheat yields, their repeated use has placed a strong selective pressure on Z. tritici and fungicide resistance is now common in field populations throughout Europe and the UK. In order to develop novel fungicides to control this disease we require detailed knowledge of genes that are essential or conditionally essential for growth and survival. The aim of this project is to establish and optimise a rapid, parallel gene-editing protocol for Z. tritici, which can be used to generate a large single-gene KO library to identify both essential and conditionally essential genes in Z. tritici.

Further reading:

  1. E.-C. Oerke. 2006. doi:10.1017/S0021859605005708
  2. M.C. McDonald, A.P. Taranto, E. Hill, et al. 2019. doi: 10.1128/mBio.01515-19
  3. Khan H., McDonald, M.C., Williams, S.J. et al. 2020. doi: /10.1186/s40694-020-00094-0
  4. Pfannenstiel BT, Zhao X, Wortman J, et al. doi: 10.1128/mBio.01246-17

BBSRC Strategic Research Priority: Sustainable Agriculture and Food: Plant and Crop Science & Understanding the Rules of Life: Microbiology & Plant Science

    Techniques that will be undertaken during the project:

    Nanopore sequencing (RNA and DNA), Hi-C, Pulse-field gel electrophoresis, CRISPR mediated DNA selection, southern hybridisation, RNA-sequencing and differential expression, Python (Jupyter), R (Stats, genome visualisation), Fluorescent microscopy, agrobacterium mediated transformation, PEG mediated transformation, DNA-RNA extraction, plant infection, microbial growth and isolation of fungi from plant tissue.

    Contact: Dr Megan McDonald, University of Birmingham