The genome sequencing and comparative analysis of a wild kiwifruit Actinidia eriantha

Kiwifruit is a widespread perennial fruit crop in the genus Actinidia. The current kiwifruit industry is mainly based on the cultivars derived from the single species Actinidia chinensis (Ac) which may bring risks such as canker disease. Introgression of desired traits from wild relatives are an important method for improving kiwifruit cultivars. In kiwifruit, A. eriantha (Ae) is a particularly important taxon used for hybridization or introgressive breeding of new kiwifruit cultivars because of its valued species-specific traits. Here, we used PacBio long reads, 10x Genomics linked reads and Hi-C map to assemble a chromosome-scale high-quality genome of Ae. Our analysis revealed that 41.3% of the genome consists of repetitive elements, comparable to the percentage in Ac. However, the genomic structural variation, including the presence/absence-variation (PAV) of genes, is distinct between Ae and Ac, despite both of them sharing the same two kiwifruit-specific whole genome duplication (WGD) events. This suggests that a post-WGD divergence mechanism occurred during their evolution. We further investigated genes involved in Ae-specific traits such as the exceptionally high content of vitamin C and the good resistance to canker disease. Finally, we found clues in relation to introgressive genome which potentially contribute to trichome trait diversity explaining diverse fruit skin types among different kiwifruit taxa. Collectively, the de novo assembled Ae genome offers valuable genomic resources to kiwifruit improvement to accelerate breeding applications.