Kiwifruit is a vital horticultural fruit crop worldwide. Abundant phenotypic variations were identified among Actinidia species, like presence and absence of indumentum on fruits and petioles, vitamin C content in fruits, disease resistance and so on. Despite the increasing availability of kiwifruit genomes and resequencing data, a comprehensive investigation of interspecific genetic diversity is lacking. 

Researchers from the Wuhan Botanical Garden of the Chinese Academy of Sciences have constructed a super pan-genome using 15 high-quality assemblies of eight Actinidia species to systematically investigate the interspecific genetic diversity in Actinidia.

This study identified a total of 61,465 gene families, and the softcore and dispensable genes were enriched in response to endogenous stimulus, response to hormone and cell wall organization or biogenesis, etc,. Moreover, this team also identified over one million structural variations (SVs) across Actinidia species, using A. chinensis ‘Donghong’ as a reference. These SVs were then used to construct a graph-based genome. Further analysis of resequencing data from 112 individuals of 20 species revealed extensive SVs probably contributing to the phenotypic diversity observed within the genus. Notably, the researchers found SV hotspot regions contributed to environmental adaptation.

Besides, resistance gene analogs (RGAs) across 15 assemblies were identified and a pan-RGA dataset was generated. One paired NLRs evolutionarily were found conserved in all the Actinidia species, exhibiting similar expression levels after Psa infection. Besides, a total of 205 gene families from pan RGA were found absent in all A. chinensis assemblies. These genes greatly enriched the disease resistance gene reservoir for future resistance breeding of kiwifruits.

In conclusion, the pan-genome construction and genetic variation identification in this study comprehensively reveal the genetic diversity of Actinidia species, which will greatly benefit the Actinidia breeding and functional genomics research.

Results have been published in Molecular Horticulture, titled “Super pan-genome reveals extensive genomic variations associated with phenotypic divergence inActinidia”. This project was supported by the National Natural Science Foundation of China, the Hubei Provincial Natural Science Foundation of China, and the Foundation of Hubei Hongshan Laboratory.

Structural variations and graph-based pan-genome of Actinidia (Image by WBG)