Legume NBS-LRR disease resistance gene content, evolution, and genomic organization at key nodes within the crop-rich Papilionoideae subfamily

The legume family contains many crops that are fundamental to agricultural systems worldwide. One important trait to study is disease resistance. Nucleotide-binding site leucine-rich repeat (NBS-LRR) encoding genes play a central role in this process. Degenerate PCR primers aimed at amplifying the NBS domain were created from NBS-LRR resistance gene homolog (RGH) sequences in the model legume Medicago truncatula (Mt). Seven Papilionoid legumes and one basal Cesalpinoid legume were targeted for amplification. Nearly 4,000 unique NBS domains were discovered. Phylogenetic analysis showed few cases of simple orthologous relationships, but relationships between groups of sequences tended to recapitulate the known phylogenetic history of the species. The data also shed light on the timing of expansions and losses of clades. Amplified NBS domains were concurrently used to query the Mt and Glycine max (Gm) genomes for RGHs. 763 Mt and 506 Gm gene models were characterized by phylogenetic analysis, domain composition, genomic distribution, and RNA-seq expression. Novel domain arrangements and non-canonical domains were identified and the origin of these structures explored. RGHs were placed within a reconstructed ancestral legume genome to enable comprehensive synteny analysis. Amplified NBS domains were additionally used to probe BAC libraries for clones containing RGHs. These were organized into contigs and singletons, and SNP discovery was initiated to map RGH clusters and integrate that data with comparative genetic maps.