Genome-wide identification and evolutionary analysis of disease resistance genes in Brassica carinata.

Brassica carinata is considered an orphan crop, yet it is vital for understanding the evolution of the triangle of U Brassica species. The availability of a genome reference for this species has allowed for the interrogation of the genomic and genetic underpinnings of important traits, including disease resistance. In this study, we report a comprehensive analysis of resistance gene analogs (RGAs) in the first genome assembly for B. carinata (zd-1). A total of 2570 RGAs were predicted, of which 2020 were transmembrane leucine-rich repeats and 550 were nucleotide-binding site leucine-rich repeats. Gene duplication events affected 65.2% of the RGAs, which were classified as either intergenomic or intragenomic duplications. The contrasting patterns of these gene duplication events between the two subgenomes (B and C) support previous findings indicating the presence of subgenome dominance in this species, a characteristic that is shared with the other allopolyploid Brassicas. Comparative analysis with its diploid progenitors, B. nigra and B.oleracea, revealed conservation of genomic features among these species, while phylogenetic analysis suggests that B. carinata RGAs have undergone extensive expansion. This study is the first to analyze the complete set of RGAs within the B. carinata genome, presenting a comprehensive view of the disease resistance landscape in this species.