Resistance gene analogue identification and comparative genomic analysis of two Brassica carinata genomes

Abstract

Brassica carinata is an allotetraploid oilseed crop with significant agronomic potential for sustainable agriculture and biofuel production due to its resilience to multiple biotic and abiotic stresses; however, comprehensive genome-wide analyses of resistance gene analogues (RGAs) remain limited. This study aimed to systematically identify and characterise RGAs in two newly assembled B. carinata genomes (C4012_v1 and 10167_v1), providing a resource to enhance disease resistance through molecular breeding and genome editing. Using comparative genomic approaches, we identified 2,498 and 2,685 RGAs in C4012_v1 and 10167_v1, respectively, including receptor-like kinases (RLKs), receptor-like proteins (RLPs), transmembrane-coiled coil proteins (TM-CCs), and nucleotide-binding site leucine-rich repeat (NLR) genes, with RLKs being the most abundant class. RGAs showed uneven distribution across B and C sub-genomes with notable chromosomal hotspots (B2, C3), and 87.9% and 89.3% of RGAs (in C4012_v1 and 10167_v1, respectively) possessed at least one additional gene copy, predominantly as intergenomic homeologous pairs ( ~ 81%) retained from the progenitor sub-genomes. Physical clustering analysis identified 216–243 RGA clusters per genome, and phylogenetic reconstruction revealed multiple clades with family-specific diversification. Comparative analysis with 49 cloned resistance genes identified 51 and 59 high-confidence homologues (CDRHs) in C4012_v1 and 10167_v1, respectively, including multiple copies of At_BAK1 (12 and 13 copies) associated with bacterial leaf spot resistance. These findings provide a comprehensive catalogue of RGAs in B. carinata , revealing their genomic organisation, duplication patterns, and evolutionary relationships, thereby offering valuable genetic resources for developing disease-resistant and resilient cultivars of this emerging oilseed crop.