Abstract

Background Canker disease caused by Pseudomonas syringae pv. actinidiae ( Psa ) poses a major threat to cultivated kiwifruit, and utilization of wild relatives are key to improve resistance. However, comprehensive comparative genomic analyses between cultivated kiwifruit and their wild relatives with enhanced resistance to Psa remain limited. Results Here we generate chromosome-scale genome assemblies for eleven wild Actinidia eriantha accessions and one interspecific hybrid between Actinidia eriantha and cultivated Actinidia chinensis var. chinensis . Integrating these with twelve previously released genomes including three Actinidia eriantha and nine Actinidia chinensis var. chinensis , we construct a reference-unbiased graph-based pangenome. These datasets reveal extensive genomic variation, including 31,790,044 SNPs, 13,512,079 InDels and 623,478 structural variations, and provide a landscape of structural variations within and between the two species. Leveraging these datasets, we identify a wild allele showing allele-specific expression, AeNLR25-1 , which enhances Psa resistance in cultivated kiwifruit. Genetic and molecular analyses demonstrate that a transposable element-induced structural variation in the AeNLR25-1 promoter introduces a species-specific WRKY binding site, conferring enhanced defense against Psa . Conclusions Pangenome across cultivated species and wild relatives provides a theoretical framework for accelerating kiwifruit genetic improvement through pangenome-enabled identification of favorable wild alleles.