Pathogenesis-related proteins are evolutionarily conserved across diploid and octoploid Fragaria species

Background: Pathogenesis-related (PR) proteins are induced in response to infection and contribute to immunity through a variety of mechanisms. To date, 19 families of PR proteins with roles in resistance to bacteria, fungi, and insects have been identified across several model and agronomically important plant species. Countless diseases threaten cultivated strawberry (Fragaria × ananassa), and identifying and characterizing PR genes in response to infection can lead to valuable new breeding targets for resistance. Results: In this study, 1060 PR genes across 16 PR families were identified in octoploid F. × ananassa, with approximately 24% of the genes organized in tandem arrays. Members of almost every PR family were found on all four subgenomes; the greatest number was typically found on the A subgenome in keeping with the hypothesis that A is the ’dominant’ subgenome in cultivated strawberry. Some gene loss occurred during polyploidization, but PR gene family size is correlated among diploid and octoploid strawberry (R2 = 0.98) and Arabidopsis thaliana (R2 = 0.95), suggesting conservation of family sizes across plant species. Strawberry PR genes have diverse domain architectures; 62.6% of the identified genes have atypical domain architectures compared to PR type members. During infection by the fungal pathogen Colletrotrichum fructicola, PR genes were dynamically expressed and distinct stages of response to infection were observed at three time points: initial induction, slight repression, and strong induction to combat pathogen spread. PR genes with known roles in response to colonization by fungal pathogens were found to be most significantly induced during the later stages of infection. Conclusions: Characterizing the genome-wide distribution and conservation of PR genes furthers our understanding of the evolution of octoploid strawberry and provides valuable insights into strawberry’s arsenal of defense against pathogens. We found subgenome dominance in octoploid strawberry affected the evolution and expression of PR genes. Strawberry PR genes with atypical domain architectures are expressed during infection, but genes with canonical architectures are the most significantly differentially expressed.