Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.
Jisen Zhang(Fujian Agriculture and Forestry University), Xingtan Zhang(Fujian Agriculture and Forestry University), Haibao Tang(Fujian Agriculture and Forestry University), Qing Zhang(Fujian Agriculture and Forestry University), Xiuting Hua(Fujian Agriculture and Forestry University), Xiaokai Ma(Fujian Agriculture and Forestry University), Fan Zhu(University of Illinois Urbana-Champaign), Tyler Jones(Hawaii Agriculture Research Center), Xin‐Guang Zhu(Chinese Academy of Sciences), John E. Bowers(University of Georgia), Ching Man Wai(Michigan State University), Chunfang Zheng(University of Ottawa), Yan Shi(Fujian Agriculture and Forestry University), Shuai Chen(Fujian Agriculture and Forestry University), Xiuming Xu(Fujian Agriculture and Forestry University), Jingjing Yue(Fujian Agriculture and Forestry University), David R. Nelson(University of Tennessee Health Science Center), Lixian Huang(Fujian Agriculture and Forestry University), Zhen Li(Fujian Agriculture and Forestry University), Huimin Xu(Fujian Agriculture and Forestry University), Dong Zhou(Fujian Agriculture and Forestry University), Yongjun Wang(Fujian Agriculture and Forestry University), Weichang Hu(Fujian Agriculture and Forestry University), Jishan Lin(Fujian Agriculture and Forestry University), Youjin Deng(Fujian Agriculture and Forestry University), Neha Pandey(University of Illinois Urbana-Champaign), Melina Cristina Mancini(University of Illinois Urbana-Champaign), D. M. de Zerpa(University of Illinois Urbana-Champaign), Julie K. Nguyen(University of Illinois Urbana-Champaign), Liming Wang(Fujian Agriculture and Forestry University), Liang Yu(University of Illinois Urbana-Champaign), Yinghui Xin(University of Illinois Urbana-Champaign), Liangfa Ge(University of Illinois Urbana-Champaign), Jie Arro(University of Illinois Urbana-Champaign), Jennifer Han(University of Illinois Urbana-Champaign), Setu Chakrabarty(University of Illinois Urbana-Champaign), Marija Pushko(University of Illinois Urbana-Champaign), Wenping Zhang(Fujian Agriculture and Forestry University), Yanhong Ma(Fujian Agriculture and Forestry University), Panpan Ma(Fujian Agriculture and Forestry University), Mingju Lv(Chinese Academy of Sciences), Fa‐Ming Chen(Chinese Academy of Sciences), Guangyong Zheng(Chinese Academy of Sciences), Jingsheng Xu(Fujian Agriculture and Forestry University), Zhenhui Yang(Fujian Agriculture and Forestry University), Fang Deng(Fujian Agriculture and Forestry University), Xuequn Chen(Fujian Agriculture and Forestry University), Zhenyang Liao(Fujian Agriculture and Forestry University), Xunxiao Zhang(Fujian Agriculture and Forestry University), Zhicong Lin(Fujian Agriculture and Forestry University), Hai Lin(Fujian Agriculture and Forestry University), Hansong Yan(Fujian Agriculture and Forestry University), Zheng Kuang(Fujian Agriculture and Forestry University), Weimin Zhong(Fujian Agriculture and Forestry University), Pingping Liang(Fujian Agriculture and Forestry University), Guofeng Wang(Fujian Agriculture and Forestry University), Yuan Yuan(Fujian Agriculture and Forestry University), Jiaxian Shi(Fujian Agriculture and Forestry University), Jinxiang Hou(Fujian Agriculture and Forestry University), Jingxian Lin(Fujian Agriculture and Forestry University), Jingjing Jin(China Tobacco), Peijian Cao(China Tobacco), Qiaochu Shen(Fujian Agriculture and Forestry University), Qingwu Jiang(Fujian Agriculture and Forestry University), Ping Zhou(Fujian Agriculture and Forestry University), Yaying Ma(Fujian Agriculture and Forestry University), Xiaodan Zhang(Fujian Agriculture and Forestry University), Rongrong Xu(Fujian Agriculture and Forestry University), Juan Liu(Fujian Agriculture and Forestry University), Yongmei Zhou(Fujian Agriculture and Forestry University), Haifeng Jia(Fujian Agriculture and Forestry University), Qing Ma(Fujian Agriculture and Forestry University), Rui Qi(Fujian Agriculture and Forestry University), Zhiliang Zhang(Fujian Agriculture and Forestry University), Jingping Fang(Fujian Agriculture and Forestry University), Hongkun Fang(Fujian Agriculture and Forestry University), Jinjin Song(Fujian Agriculture and Forestry University), Mengjuan Wang(Fujian Agriculture and Forestry University), Guangrui Dong(Fujian Agriculture and Forestry University), Gang Wang(Fujian Agriculture and Forestry University), Zheng Chen(Fujian Agriculture and Forestry University), Teng Ma(Fujian Agriculture and Forestry University), Hong Liu(Fujian Agriculture and Forestry University), Singha R. Dhungana(University of Missouri), Sarah E. Huss(University of Illinois Urbana-Champaign), Xiping Yang(University of Florida), Anupma Sharma(Texas A&M University System), Jhon H. Trujillo(Centro de Investigación de la Caña de Azúcar de Colombia), Maria Cristina Martinez(Centro de Investigación de la Caña de Azúcar de Colombia), Matthew E. Hudson(University of Illinois Urbana-Champaign), John J. Riascos(Centro de Investigación de la Caña de Azúcar de Colombia), Mary A. Schuler(University of Illinois Urbana-Champaign), Li‐Qing Chen(University of Illinois Urbana-Champaign), David Braun(University of Missouri), Lei Li(Fujian Agriculture and Forestry University), Qingyi Yu(Texas A&M University System), Jianping Wang(University of Florida), Kai Wang(Fujian Agriculture and Forestry University), Michael C. Schatz(Johns Hopkins University), David Heckerman(Microsoft (United States)), Marie‐Anne Van Sluys(Universidade de São Paulo), Gláucia Mendes Souza(Universidade de São Paulo), Paul H. Moore(Hawaii Agriculture Research Center), David Sankoff(University of Ottawa), Robert VanBuren(Michigan State University), Andrew H. Paterson(University of Georgia), Chifumi Nagai(Hawaii Agriculture Research Center), Ray Ming(University of Illinois Urbana-Champaign)
Cited by 789Open Access
Abstract
Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.
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