Chromosome-level genome assembly reveals the genetic mechanisms underlying elite waterlogging tolerance in Actinidia rufa

Abstract Actinidia rufa is a valuable species for hybridization and introgressive breeding of new kiwifruit cultivars due to its exceptional tolerance to waterlogging. In this study, a chromosome-level genome of A. rufa was assembled using Illumina short-read and PacBio Continuous Long Read (CLR) sequencing technologies. The assembled genome spans 613.66 Mb with an N50 of 3.06 Mb, and 94 scaffolds were anchored to 29 pseudochromosomes. A total of 42,484 protein-coding genes and 267.26 Mb of repetitive sequences, accounting for 49.08% of the genome, were identified. Phylogenetic analysis demonstrated a close evolutionary relationship between A. rufa and A. chinensis, with their most recent common ancestor being estimated to diverge around 7 million years ago. Demographic analysis indicated a historical population expansion in A. rufa, whose current suitable habitats are primarily found in the Japanese archipelago and Taiwan, China. Comparative genomic analysis revealed large-scale structural variations, including a chromosomal region on Chr19 in A. rufa that corresponds to two distinct segments on Chr2 and Chr9 in A. chinensis. Additionally, A. rufa cv. ‘MTS7001’ exhibited superior waterlogging tolerance compared to A. chinensis cv. ‘Donghong’. Gene expression analysis showed that, in response to early waterlogging stress, A. rufa exhibited upregulation of genes associated with energy metabolism and signaling of hormones, including those related to auxin, abscisic acid, and brassinosteroids, compared to A. chinensis. This study provides genomic insights into the genetic basis of exceptional waterlogging tolerance in A. rufa, contributing to molecular breeding efforts in kiwifruits in the future.