Defensive diminishment: A chromosome-scale reference genome assembly of pigeonpea wild relative Cajanus platycarpus (Benth.) highlights the evolutionary decline of defence genes in Cajanus cajan (L.)

Plants evolve diverse genetic adaptations to survive varied environmental stresses. Cajanus platycarpus, a wild relative of pigeonpea (Cajanus cajan), exhibits remarkable resilience to multiple abiotic and biotic stresses. However, the genomic basis of this broad-spectrum adaptability remains poorly understood. Besides, it is also pertinent to unravel, how domestication has altered genetic diversity in C. cajan. Here, we present the first high-quality, chromosome-scale reference genome of C. platycarpus, providing novel insights into stress adaptability. We assembled a 482.2 Mb genome comprising of 11 chromosomes (N50: 48 Mb) and a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 95.2%. Annotation demonstrated higher gene number and density compared to its cultivated counterpart. This was apparently attributed to segmental duplication (SD) which revealed 12,773 genic SDs. Gene family evolutionary analysis identified extensive expansion of stress-responsive genes in C. platycarpus. Structural variations between C. platycarpus and C. cajan revealed major changes in upstream elements signifying contrasting gene regulation. Notably, higher number of key resistance (R) genes, including nucleotide-binding site-leucine-rich repeat (NLR), leucine-rich repeat receptor-like kinase/protein (LRR-RLK/RLP) families, were seen in the wild relative contributing to enhanced stress perception and response. Comparative genomics with C. cajan revealed notable variations in the inceptin receptor (INR) genes of C. platycarpus, offering novel insights into its potentially superior ability to perceive Helicoverpa armigera, a major pigeonpea herbivore. The C. platycarpus genome provides a valuable resource for understanding the genetic basis of stress resilience in the wild Cajanus species. These findings offer crucial leads into adaptive evolution and lay the much-required foundation for translational utility.