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  Haplotype-resolved sweet potato genome traces back its hexaploidization history

Yang, J., Moeinzadeh, M. H., Kuhl, H., Helmuth, J., Xiao, P., Haas, S., et al. (2017). Haplotype-resolved sweet potato genome traces back its hexaploidization history. Nature Plants, 2017(3), 696-703. doi:10.1038/s41477-017-0002-z.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002D-DA32-C Version Permalink: http://hdl.handle.net/21.11116/0000-0001-4304-F
Genre: Journal Article

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 Creators:
Yang, Jun, Author
Moeinzadeh, Mohammad Hossein1, Author              
Kuhl, Heiner, Author
Helmuth, Johannes2, Author              
Xiao, Peng , Author
Haas, Stefan3, Author              
Liu, Guiling , Author
Zheng, Jianli , Author
Sun, Zhe, Author
Fan, Weijuan, Author
Deng, Gaifang , Author
Wang, Hongxia , Author
Hu, Fenhong, Author
Zhao, Shanshan , Author
Fernie, Alisdair R. , Author
Börno, Stefan T.4, Author              
Timmermann, Bernd4, Author              
Zhang, Peng , Author
Vingron, Martin5, Author              
Affiliations:
1Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              
2Computational Epigenetics (Ho-Ryun Chung), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479658              
3Gene Structure and Array Design (Stefan Haas), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479640              
4Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479670              
5Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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 Abstract: 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.

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Language(s): eng - English
 Dates: 2017-08-21
 Publication Status: Published online
 Pages: 8
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 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.1038/s41477-017-0002-z
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Title: Nature Plants
Source Genre: Journal
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Publ. Info: Nature Publishing Group
Pages: - Volume / Issue: 2017 (3) Sequence Number: - Start / End Page: 696 - 703 Identifier: ISSN: 2055-0278
CoNE: /journals/resource/2055-0278