Chromosome-level genome assembly of the autotetraploid yellow pitaya provides novel insights into evolution of trait patterning in pitaya species with different ploidy

Yellow pitaya (Selenicereus megalanthus, 2n = 4x = 44) breeding remains severely hindered due to the lack of a reference genome. Here, we present a high-quality chromosome-level genome assembly of yellow pitaya using PacBio HiFi sequencing and Hi-C scaffolding technologies. We identify yellow pitaya as an autotetraploid with a genome size of 1.79 Gb, harboring 27,246 high-confidence genes probably from diploid ancestors, red pitaya (S. undatus). By comparative analysis of the 3D chromatin architecture, we identify varying number of compartment A/B, topologically associated domains (TADs), and structural variations in diploid (red pitaya) and polyploid (yellow pitaya) species. We find that TAD boundaries are enriched with transcription factor motifs in both species. We find significant alterations in expression of genes in the betalain biosynthesis pathway in both species. We detect differential expression of genes encoding key regulators of pericarp color within the TAD regions of polyploid pitaya and diploid pitaya. We also identify the expression differences in candidate genes that likely influence betacyanin and betaxanthin synthesis in both species. Our findings suggest that differential 3D genome organization, especially differences in TAD boundaries, may impact gene expression, which may further lead to different trait formation in different pitaya species. This provides theoretical implications for fast-forward breeding.