Haplotype-resolved sweet potato genome traces back its hexaploidization history

Here we present the 15 pseudochromosomes of sweet potato, Ipomoeabatatas, the seventh most important crop in the world and the fourth most significant in China. By using a novel haplotypingmethod based on genomeassembly, we have produced a half haplotype-resolved genomefrom ~296 Gb of paired-end sequence reads amounting to roughly 67-fold coverage. By phylogenetic treeanalysis of homologous chromosomes, it was possible to estimate the time of two recent whole- genomeduplication events as occurring about 0.8 and 0.5 million years ago. This half haplotype-resolved hexaploid genomerepresents the first successful attempt to investigate the complexity of chromosome sequence composition directly in a polyploid genome, using sequencing of the polyploidorganism itself rather than any of its simplified proxy relatives. Adaptation and application of our approach should provide higher resolution in future genomicstructure investigations, especially for similarly complex genomes.