PT  - JOURNAL ARTICLE
AU  - Jun Yang
AU  - M-Hossein Moeinzadeh
AU  - Heiner Kuhl
AU  - Johannes Helmuth
AU  - Peng Xiao
AU  - Guiling Liu
AU  - Jianli Zheng
AU  - Zhe Sun
AU  - Weijuan Fan
AU  - Gaifang Deng
AU  - Hongxia Wang
AU  - Fenhong Hu
AU  - Alisdair R Fernie
AU  - Bernd Timmermann
AU  - Peng Zhang
AU  - Martin Vingron
TI  - The haplotype-resolved genome sequence of hexaploid <em>Ipomoea batatas</em> reveals its evolutionary history
AID  - 10.1101/064428
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 064428
4099  - http://biorxiv.org/content/early/2016/07/18/064428.short
4100  - http://biorxiv.org/content/early/2016/07/18/064428.full
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.