A chromosome-scale reference genome assembly of pigeonpea wild relative Cajanus platycarpus highlights the evolutionary decline of defence genes in Cajanus cajan

Abstract Plants exhibit diverse genetic adaptations to withstand environmental stresses. Cajanus platycarpus, a wild relative of pigeonpea (Cajanus cajan), shows remarkable tolerance to multiple abiotic and biotic stresses, yet the genomic basis of this resilience remains poorly understood. Here, we report the first high-quality, chromosome-scale reference genome of C. platycarpus (482.2 Mb; 11 chromosomes; N50: 48 Mb; BUSCO score: 95.2%). Compared with cultivated pigeonpea, C. platycarpus exhibits a higher gene number and density, largely due to 12 773 genic segmental duplications. Gene family analyses revealed significant expansion of stress-responsive genes, particularly those associated with defence. Structural variations with C. cajan highlighted major differences in upstream regulatory regions, suggesting altered gene regulation. Notably, key resistance genes, including nucleotide-binding site–leucine-rich repeat and leucine-rich repeat receptor-like kinase/protein families, were seen to be more in the wild relative, contributing to enhanced stress perception and response. Divergence in inceptin receptor genes between the two species offered insights into the potentially superior ability of the wild species to recognize herbivory by Helicoverpa armigera, a key pigeonpea pest. The C. platycarpus genome offers crucial insights into the genetic basis of stress resilience and adaptive evolution in wild Cajanus species, laying a strong foundation for their translational utility in crop improvement.