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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. The pace at which these pathogens evade these control strategies often exceeds our ability to develop new chemical technologies or plant varieties to counter the pathogen’s evolution. 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.

Whole genome sequencing with long-read technologies, PacBio SMRT and Oxford Nanopore, have enabled cheap and fast sequencing and assembly of small microbial genomes to the chromosomal level. While fungal geneticists have known for many decades that “hard to assemble”, repetitive regions of chromosomes harbour pathogenicity genes, comprehensive investigation of these regions was restricted due to our inability to assemble these regions into chromosomes with short-read sequencing technologies. This limitation no longer exists. Long-read sequencing studies on pathogenic fungi have revealed large chromosomal re-arrangements, chromosomal gains and deletions are commonplace in plant pathogenic fungi. This extreme level of chromosomal plasticity is also observed in other disease-causing organisms, such as cancer cells and drug-resistant human fungal pathogens. There is now growing evidence that the ability of these organisms to rapidly re-arrange their chromosomes, enables these pathogens to continually evade host immune responses and chemical control.

The current research program in the McDonald Lab focuses on rapidly evolving regions of fungal pathogen genomes that are enriched in repetitive DNA (transposons) and contain known pathogenicity genes. These pathogenicity genes can be translocated across chromosomes and horizontally transferred between different pathogen species. 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).

PhD Project

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

This project will characterise the extent and frequency of these rapid chromosomal rearrangements in three fungal wheat pathogens (Bipolaris sorokiniana, Pyrenophora tritici-repentis and Parastagonospora nodorum). This will involve whole-genome resequencing of a global collection of fungal isolates, followed by comprehensive genome and transposon annotation. This project will characterise chromosomal plasticity using long-read whole genome sequencing coupled with 3D genome re-construction techniques (known as Hi-C). Later stages of the project will use fluorescent imaging to validate chromosomal interactions observed in the sequencing data with live-cell imaging. These techniques all require infrastructure that currently exists within the School of Biosciences.

References:

  1. E.-C. Oerke. 2006. Crop losses due to pests. J. of Agr. Sci., 144, 31–43. doi:10.1017/S0021859605005708
  2. M.C. McDonald, A.P. Taranto, E. Hill, et al. 2019. Transposon-mediated horizontal transfer of the host-specific virulence protein ToxA between three fungal wheat pathogens. mBio, 10 (5) e01515-19; doi: 10.1128/mBio.01515-19

BBSRC Strategic Research Priority: Sustainable Agriculture and Food: Plant and Crop 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, plant infection, microbial growth and isolation of fungi from plant tissue

    Contact: Dr Megan McDonald, University of Birmingham