The avocado pangenome reveals dynamic clustering and lineage-specific diversity of NLR genes

Avocado is an economically important perennial tree crop with a complex domestication history, yet modern genomic resources are limited. We present the first high-quality avocado pangenome, spanning seven diverse accessions across Mexican, Guatemalan, and West-Indian lineages. PacBio HiFi, partially phased assemblies deliver near chromosome-level continuity (N50 ~57 Mb; BUSCO >96%), and functional annotations show enrichment of immune-related families. Core–accessory partitioning indicates adaptive functions — pathogen response and secondary metabolism — are overrepresented in accessory genes. Nucleotide-binding Leucine-rich repeat ( NLR ) genes were catalogued (226–256 per accession), showing lineage-specific expansions, diverse domain architectures, and frequent chromosomal clustering. Structural variants concentrate within NLR loci, marking hotspots of pathogen-detection diversification. Comparative analyses show ~54% of NLRs are shared, with extensive functional and sequence diversity among accessions. Together, these results define the avocado NLRome and its core– accessory interplay, providing a graph-based framework to accelerate discovery of resistance loci and breeding for durable disease resistance.