Haplotype-resolved sweet potato genome traces back its hexaploidization history

被引：0
作者：
Jun Yang
M-Hossein Moeinzadeh
Heiner Kuhl
Johannes Helmuth
Peng Xiao
Stefan Haas
Guiling Liu
Jianli Zheng
Zhe Sun
Weijuan Fan
Gaifang Deng
Hongxia Wang
Fenhong Hu
Shanshan Zhao
Alisdair R. Fernie
Stefan Boerno
Bernd Timmermann
Peng Zhang
Martin Vingron
机构：
[1] Chinese Academy of Sciences,Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center
[2] Shanghai Chenshan Botanical Garden,Department of Computational Molecular Biology
[3] Max Planck Institute for Molecular Genetics,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences
[4] Institute of Plant Physiology and Ecology,Department of Molecular Physiology
[5] Shanghai Institutes for Biological Sciences,undefined
[6] Chinese Academy of Sciences,undefined
[7] Max Planck Institute of Molecular Plant Physiology,undefined
[8] Tai’an Academy of Agricultural Sciences,undefined
[9] Max Planck Institute for Molecular Genetics,undefined
[10] Sequencing Core Facility,undefined
[11] Max Planck Institute for Molecular Genetics,undefined
[12] Otto-Warburg-Laboratory: Computational Epigenomics Group,undefined
来源：
Nature Plants | 2017年 / 3卷
关键词：
D O I：
暂无
中图分类号：
学科分类号：
摘要：
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.
引用
收藏
页码：696 / 703
页数：7
相关论文
共 80 条
[1]  
Ozias-Akins P(1994)Nuclear DNA content and ploidy levels in the genus Ipomoea J. Am. Soc. Hortic. Sci. 119 110-115
[2]  
Jarret RL(1997)Autopolyploidy versus allopolyoloidy and low-density randomly amplified polymorphic DNA linkage maps of sweetpotato J. Am. Soc. Hortic. Sci. 122 822-828
[3]  
Ukoskit K(2003)A genetic linkage map of sweetpotato ( Mol. Breeding 11 169-185
[4]  
Thompson PG(2015) (L.) Lam.) based on AFLP markers DNA Res. 22 171-179
[5]  
Kriegner A(2011)Survey of genome sequences in a wild sweet potato, Nature 475 189-195
[6]  
Cervantes JC(2015) (H. B. K.) G. Don Nat. Biotechnol. 33 524-530
[7]  
Burg K(2012)Genome sequence and analysis of the tuber crop potato Nat. Genet. 44 1098-1103
[8]  
Mwanga ROM(2014)Genome sequence of cultivated Upland cotton ( Nat. Genet. 46 567-572
[9]  
Zhang D(2013) TM-1) provides insights into genome evolution Nature 496 87-90
[10]  
Hirakawa H(2013)The draft genome of a diploid cotton Nature 496 91-95
12345678