The work aims to apply sequencing technologies and ‘-omics’ approaches to understand the cause of the differences in the ability of isolates of the oomycete pathogen Phytophthora fragariae to cause disease in varieties of the cultivated strawberry Fragaria × ananassa. This will aid in the understanding of the resistance response and aid in the breeding of resistant plant material. To achieve this, we will:
- Infect plants carrying known resistance genes with isolates of P. fragariae to confirm their pathogenicity race.
- Sequence isolates of different pathogenicity of both P. fragariae and the closely related raspberry pathogen Phytophthora rubi with short read Illumina sequencing.
- Sequence one isolate of P. fragariae with long read PacBio sequencing, to produce a reference assembly.
- Assemble and annotate the genomes of all sequenced isolates to identify any genes unique to a particular pathogenicity race.
- Identify potential effector genes in the genomes of the pathogen, mostly of the RxLR and crinkler classes.
- Sequence RNA from isolates of different races to aid in genome annotation and to investigate which genes are active during pathogenicity.
- Call variant sites, including single base changes, small insertions and deletions and larger structural variants to understand the population structure within this species.
- Identify candidate genes that may be recognised by a resistant plant and confirm the absence of expression of this gene in isolates of other races.
PhD Student: Thomas M. Adams
PhD Supervisors: Dr. Charlotte F. Nellist, Dr. Richard J. Harrison, Prof. Jim M. Dunwell
Duration: 2015 – 2018