Pathogenomics of Phytophthora fragariae, the causal agent of strawberry red core disease

Strawberries are a valuable fruit crop for the UK and worldwide. The UK berry market was worth £1.2 billion in 2016, with strawberries as 50% of this market. One of the major threats to the industry is the water-borne disease strawberry red core, caused by the oomycete pathogen Phytophthora fragariae. One way to increase the resilience of the industry to this pathogen is breeding for genetic resistance in plants. To do this effectively, a strong understanding of the pathogen, including identification of avirulence genes is required. To investigate this, ten isolates of P. fragariae and three isolates of the related raspberry pathogen Phytophthora rubi were sequenced with the Illumina MiSeq system. PacBio sequencing was used on an additional isolate of P. fragariae, BC-16, to produce an improved reference assembly of 91 Mb in 180 contigs. Following assembly of these genomes and gene prediction through RNA-Seq guided and ab initio methods, effector genes were identified. Further investigations utilising orthology analysis, variant calling and differential expression analysis allowed for the identification of candidate avirulence genes for races UK1, UK2 and UK3. A very strong candidate for the avirulence gene in the UK2 race was identified as an RxLR effector named g27513 in BC-16. Further investigations did not identify clear cis or trans DNA sequence polymorphisms causing the variation in expression across races. Three of the identified races (UK1, UK2 and UK3) clustered into a single population with low levels of nucleotide diversity and a mixture of clonal and sexual reproduction which may possibly be undergoing recovery from a recent genetic bottleneck. The candidate genes provide future targets for identifying avirulence genes to aid in effector guided breeding approaches to produce disease resistant strawberry plants. This work also provides resources for further investigations of this pathosystem and the Phytophthora genus as a whole.