Genomics of Phytophthora fragariae

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

Screen Shot 2018-01-23 at 21.47.01

The life cycle of Phytophtora fragariae, showing the ability of the pathogen to cause disease that results in the death of the plant, as well as its ability to remain in the soil in a latent state.

Screen Shot 2018-01-23 at 21.47.08

Plant varieties resistant to multiple races of Phytophthora fragariae can be bred through crossing of varieties containing one or more resistant genes.

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