Local gene duplications drive extensive NLR copy number variation across multiple genotypes of Theobroma cacao

Nucleotide-binding leucine-rich repeat receptors (NLR) are an essential component of plant immunity. NLR evolution is complex and dynamic, with rapid expansions, contractions, and polymorphism. Hundreds of high-quality plant genomes generated over the last 2 decades provide substantial insight into the evolutionary dynamics of NLR genes. Despite steadily decreasing sequencing costs, the difficulty of sequencing, assembling, and annotating high-quality genomes has resulted in comparatively little genome-wide information on intraspecies NLR diversity in long-lived perennial species. In this study, we investigated the evolution of NLR genes across 11 high-quality genomes of the chocolate tree, Theobroma cacao L. We found 3-fold variation in NLR copy number across genotypes, a pattern driven primarily by expansion of NLR clusters via tandem and proximal duplication. Our results indicate local duplications can radically reshape gene families over short evolutionary time scales, creating extensive intraspecific variation and a source of NLR diversity that could be utilized to enrich our understanding of both plant–pathogen interactions and resistance breeding.