Haplotype-resolved sweet potato genome traces back its hexaploidization history

Yang, Jun; Moeinzadeh, Mohammad Hossein; Kuhl, Heiner; Helmuth, Johannes; Xiao, Peng; Haas, Stefan; Liu, Guiling; Zheng, Jianli; Sun, Zhe; Fan, Weijuan; Deng, Gaifang; Wang, Hongxia; Hu, Fenhong; Zhao, Shanshan; Fernie, Alisdair R.; Börno, Stefan T.; Timmermann, Bernd; Zhang, Peng; Vingron, Martin

doi:10.1038/s41477-017-0002-z

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Haplotype-resolved sweet potato genome traces back its hexaploidization history

MPS-Authors

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Moeinzadeh, Mohammad Hossein
Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Helmuth, Johannes
Computational Epigenetics (Ho-Ryun Chung), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Haas, Stefan
Gene Structure and Array Design (Stefan Haas), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Börno, Stefan T.
Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Timmermann, Bernd
Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Vingron, Martin
Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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引用

Yang, J., Moeinzadeh, M. H., Kuhl, H., Helmuth, J., Xiao, P., Haas, S., Liu, G., Zheng, J., Sun, Z., Fan, W., Deng, G., Wang, H., Hu, F., Zhao, S., Fernie, A. R., Börno, S. T., Timmermann, B., Zhang, P., & Vingron, M. (2017). Haplotype-resolved sweet potato genome traces back its hexaploidization history. Nature Plants, 2017(3), 696-703. doi:10.1038/s41477-017-0002-z.

引用: https://hdl.handle.net/11858/00-001M-0000-002D-DA32-C

要旨

Here we present the 15 pseudochromosomes of sweet potato, Ipomoea batatas, the seventh most important crop in the world and the fourth most significant in China. By using a novel haplotyping method based on genome assembly, we have produced a half haplotype-resolved genome from ~296 Gb of paired-end sequence reads amounting to roughly 67-fold coverage. By phylogenetic tree analysis of homologous chromosomes, it was possible to estimate the time of two recent whole-genome duplication events as occurring about 0.8 and 0.5 million years ago. 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 sequencing of the polyploid organism itself rather than 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.Assembly of polyploid plant genomes has been technically challenging. Now, a study presents a half haplotype-resolved hexaploid genome of sweet potato, Ipomoea batatas, using a novel haplotyping method.