A haplotype-resolved chromosome-level genome assembly for the hexaploid Jerusalem artichoke provides insights into its origin, evolution and inulin metabolism

Jerusalem artichoke (Helianthus tuberosus) is a global multifunctional crop with wide applications in the food, health, feed and biofuel industries and ecological protection; it also serves as a germplasm pool for the breeding of the global oil crop common sunflower (Helianthus annuus). However, biological studies on Jerusalem artichoke have been hindered by the lack of genome sequences, and genome assembly has been challenging due to high polyploidy and a large genome size. Here, we report the 21 Gb chromosome-level hexaploid-genome assembly of Jerusalem artichoke, comprising 17 homologous groups, each with 6 pseudochromosomes. We found multiple large-scale chromosome rearrangements between Jerusalem artichoke and common sunflower, and our results show that the hexaploid genome of Jerusalem artichoke was formed by a hybridization event between a tetraploid and a diploid Helianthus species, followed by chromosome doubling of the hybrid, which occurred approximately 2 million years ago. Moreover, we identified more copies of actively expressed genes involved in inulin metabolism and elucidated that these genes may still be undergoing the process of loss-function, sub- or neo-functionalization. These genomic resources will promote further biological studies, breeding improvement, and industrial utilization of Helianthus crops.