RosaR80: A New Framework for the Comparative Analysis of Disease Resistance Genes in the Rosaceae - Apple, Peach, Strawberry

Routine whole-genome sequencing has facilitated highly focused comparative analysis of gene families across multiple related taxa. The Rosaceae plant family includes several species of significance to human endeavors, and may benefit from insights gained using such comparative methods, including high-throughput gene discovery and targeted allele mining for plant improvement. The RosaR80 framework is a novel, robust approach to categorizing NB-LRR disease resistance genes for cross-species evolutionary analysis in the Rosaceae. We created a standardized pipeline to extract and annotate NB-LRR genes from publicly available genome sequences of apple, peach and strawberry. Homology groups were defined at an 80% NB DNA identity threshold (Rosaceae Resistance genes at 80% identity). Phylogenetic analysis of the resulting datasets was used to visualize allele diversification patterns and R locus attributes across species. R genes have diversified significantly between the species analyzed, with widely varying representation across the three genomes. Apple accounts for the majority of species-specific RosaR80 lineages. Consistent with current phylogeny, most shared lineages are between apple and peach, with only five lineages shared between all three species. Patterns of R gene evolution suggest that, in response to pathogens, strawberry evolved broad representation of distinct R gene lineages with low levels of allelic diversification, while peach and particularly apple developed high levels of allelic diversification within several lineages. We speculate that these diversified species-specific lineages are actively evolving in response to selection by pathogens. The RosaR80 framework may allow for a more targeted approach to identifying alleles useful for plant improvement programs.