An international team of researchers from the Chenshan Botanical Garden (CSBG) in Shanghai, the Max Planck Institute for Molecular Genetics (MPIMG) in Berlin, the Shanghai Institute of Plant Physiology and Ecology (SIPPE), the Max Planck Institute of Molecular Plant Physiology (MPIMP) in Potsdam, the Tai’an Academy of Agricultural Sciences (TAAS) in Shandong, has been able to sequence and phase the sweet potato genome. The results of the study, published today in Nature Plants, shed light on the evolutionary history of the sweet potato.
With a consistent global annual production of more than 100 million tons, the sweet potato, Ipomoea batatas, is an important source of calories, proteins, vitamins and minerals for humanity. It is the seventh most important crop in the world and the fourth most significant crop of China.
Sweet potato has the most complicated genome among flowering plants in the Convolvulaceae family, being hexaploid and having 90 chromosomes (2n = 6x = 90). With the novel haplotyping method developed in the study, scientists demonstrated that 30 chromosomes came from the diploid progenitor of sweet potato and the other 60 chromosomes came from the tetraploid progenitor. The modern cultivated sweet potato originated from a crossing between the diploid and tetraploid progenitors about 500,000 years ago following an whole genome duplication event. The results not only revealed the mysterious origination of hexaploid sweet potato, but also accelerated the further utilization of wild relatives of sweet potato.
There are 78,781 gene models from 49,063 gene loci in current assembly. The study also showed that due to functional redundancy among the six homologous chromosomes in the hexaploid organism, quite a number of the genes have deleterious mutations in different alleles, such as a high frequency of frameshift events identified in the phased six haplotypes. The result indicated that the natural selection pressure on particular genes in the hexaploid organism is much lower than those in diploid organisms, which also provides the basis for faster genome evolution in the polyploid organisms.
Many gene clusters were found in the current genome assembly, indicating that pathway regulation via clustered genes is commonly used in the genus Ipomoea. Although all the orthologous genes found are based on protein sequence similarity, their biological functions are not necessarily the same as those reported for similar gene clusters in other species. Nevertheless, the identified gene clusters in I. batatas open up possibilities for investigating metabolic regulatory mechanisms in this plant.
Overall, the methodology presented in the paper is an important advance in the genomic analysis of polyploid organisms. Meanwhile, the haplotype-resolved genome sequence of sweet potato already begins the era of precise genome manipulation for this human food resource.
Sponsors of the study
Alexander von Humboldt Foundation
IMPRS-CBSC doctoral program
International Science & Technology Cooperation Program of China
National Natural Science Foundation of China
National High Technology Research and Development Program of China
Chinese Academy of Sciences
China Postdoctoral Science Foundation
Shanghai Municipal Afforestation & City Appearance and Environmental Sanitation Administration
Science and Technology Commission of Shanghai Municipality
For more information
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. Haplotype-resolved sweet potato genome traces back its hexaploidization history. Nature Plants, 2017; DOI: 10.1038/41477-017-0002.