Phased chromosome-level genome assembly provides insight into the origin of hexaploid sweetpotato

Abstract The hexaploid sweetpotato ( Ipomoea batatas [L.] Lam.) is a globally important stable crop and plays a significant role in biofortification. The high resilience and adaptability of sweetpotato provide it with advantages in addressing food security and climate change issues. Here we report a haplotype-resolved chromosome-level genome assembly of an African cultivar, ‘Tanzania’, which enables ancestry inference along the haplotype-phased chromosomes. Our analyses reveal that the wild tetraploid I. aequatoriensis , currently found in coastal Ecuador, is the closest known relative of sweetpotato and likely a direct descendant of one of the sweetpotato progenitors. The other unknown progenitor(s) of sweetpotato have a closer genetic relationship to the wild tetraploid I. batatas 4×, distributed in Central America, than to I. aequatoriensis . The different ancestral sequences are not distributed in typical subgenomes but are intertwined on the same chromosomes, possibly due to the known non-preferential recombination among haplotypes. Although I. batatas 4× was not involved in the hexaploidization event, introgression from I. batatas 4× to the hexaploid sweetpotato is evident. Our study improves our understanding of sweetpotato origin and provides valuable genomic resources to accelerate sweetpotato breeding.