RT Journal Article SR Electronic T1 The haplotype-resolved genome sequence of hexaploid Ipomoea batatas reveals its evolutionary history JF bioRxiv FD Cold Spring Harbor Laboratory SP 064428 DO 10.1101/064428 A1 Jun Yang A1 M-Hossein Moeinzadeh A1 Heiner Kuhl A1 Johannes Helmuth A1 Peng Xiao A1 Guiling Liu A1 Jianli Zheng A1 Zhe Sun A1 Weijuan Fan A1 Gaifang Deng A1 Hongxia Wang A1 Fenhong Hu A1 Alisdair R Fernie A1 Bernd Timmermann A1 Peng Zhang A1 Martin Vingron YR 2016 UL http://biorxiv.org/content/early/2016/07/18/064428.abstract AB Although the sweet potato, Ipomoea batatas, is the seventh most important crop in the world and the fourth most significant in China, its genome has not yet been sequenced. The reason, at least in part, is that the genome has proven very difficult to assemble, being hexaploid and highly polymorphic; it has a presumptive composition of two B1 and four B2 component genomes (B1B1B2B2B2B2). By using a novel haplotyping method based on de novo genome assembly, however, we have produced a half haplotype-resolved genome from ∼267Gb of paired-end sequence reads amounting to roughly 60-fold coverage. By phylogenetic tree analysis of homologous chromosomes, it was possible to estimate the time of two whole genome duplication events as occurring about 525,000 and 341,000 years ago. Our analysis also identified many clusters of genes for specialized compounds biosynthesis in this genome. This half haplotype-resolved hexaploid genome represents the first successful attempt to investigate the complexity of chromosome sequence composition directly in a polyploid genome, using direct sequencing of the polyploid organism itself rather than of any of its simplified proxy relatives. Adaptation and application of our approach should provide higher resolution in future genomic structure investigations, especially for similarly complex genomes.