Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping

Abstract

Background

Kiwifruit ( Actinidia spp.) is a dioecious plant with fruits containing abundant vitamin C and minerals. A handful of kiwifruit species have been domesticated, among which Actinidiaeriantha is increasingly favored in breeding owing to its superior commercial traits. Recently, elite cultivars from A. eriantha have been successfully selected and further studies on their biology and breeding potential require genomic information, which is currently unavailable.

Findings

We assembled a chromosome-scale genome sequence of A. eriantha cultivar White using single-molecular sequencing and chromatin interaction map–based scaffolding. The assembly has a total size of 690.6 megabases and an N50 of 21.7 megabases. Approximately 99% of the assembly were in 29 pseudomolecules corresponding to the 29 kiwifruit chromosomes. Forty-three percent of the A. eriantha genome are repetitive sequences, and the non-repetitive part encodes 42,988 protein-coding genes, of which 39,075 have homologues from other plant species or protein domains. The divergence time between A. eriantha and its close relative Actinidia chinensis is estimated to be 3.3 million years, and after diversification, 1,727 and 1,506 gene families are expanded and contracted in A. eriantha, respectively.

Conclusions

We provide a high-quality reference genome for kiwifruit A. eriantha. This chromosome-scale genome assembly is substantially better than 2 published kiwifruit assemblies from A. chinensis in terms of genome contiguity and completeness. The availability of the A. eriantha genome provides a valuable resource for facilitating kiwifruit breeding and studies of kiwifruit biology.