Genome-Wide Identification and Comparative Evolutionary Analysis of NLR Genes in Cajanus cajan

Abstract

Cajanus cajan (L.) commonly known as pigeon pea is a vital leguminous crop renowned for its nutritional and agronomic value. However, its productivity is severely constrained by biotic stresses, particularly the pod borer Helicoverpa armigera. Understanding the genetic basis of host resistance is essential for developing resilient cultivars. In this study, a comprehensive genome-wide exploration of nucleotide-binding site leucine-rich repeat (NLR) genes was conducted in C. cajan to elucidate their structural diversity and evolutionary patterns. Using the NLRtracker pipeline integrated with the RefPlantNLR database, 205 NLR homologs were identified and classified into four subclasses: CC-NLR, TIR-NLR, CCG10-NLR and CCR-NLR. Among these, CC-NLR (84 genes) and TIR-NLR (88 genes) were predominant indicating their major role in immune signaling. Multiple sequence alignment revealed conserved FLY motifs within the NBARC domain, suggesting evolutionary conservation across NLR families. Phylogenetic and duplication analyses highlighted dynamic gene birth–death events and lineage-specific expansions, reflecting adaptive diversification under selective pressure. These findings enhance the understanding of NLR evolution in C. cajan and provide a valuable foundation for molecular breeding aimed at improving disease resistance and crop productivity.