Resistance gene analogs in the Brassicaceae: Identification, characterization, distribution, and evolution

The Brassicaceae consists of a wide range of species, including important Brassica crop species and the model plant Arabidopsis thaliana. Brassica crop diseases impose significant yield losses annually. A major way to reduce susceptibility to disease is the selection in breeding for resistance gene analogs (RGAs). Nucleotide-binding site-leucine-rich repeat (NLR), receptor-like kinases (RLK), and receptor-like proteins (RLP) are the main types of RGAs; they contain conserved domains and motifs and play specific roles in resistance to pathogens. Here, all classes of RGAs have been identified using annotation and assembly-based pipelines in all available genome annotations from the Brassicaceae, including multiple genome assemblies of the same species where available (total of 32 genomes). The number of RGAs, based on genome annotations, varies within and between species. In total 34,065 RGAs were identified with the majority being RLKs (21,691), then NLRs (8,588) and RLPs (3,786). Analysis of the RGA protein sequences revealed a high level of sequence identity, whereby 99.43% of RGAs fell in several orthogroups. This study establishes a resource for the identification and characterization of RGAs in the Brassicaceae and provides a framework for further studies of RGAs for an ultimate goal of assisting breeders in improving resistance to plant disease.