Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L

• Published in: Nature genetics Vol. 50; no. 11; pp. 1565 - 1573
• Main Authors: Zhang, Jisen, Zhang, Xingtan, Tang, Haibao, Zhang, Qing, Hua, Xiuting, Ma, Xiaokai, Zhu, Fan, Jones, Tyler, Zhu, Xinguang, Wai, Ching Man, Chen, Shuai, Xu, Xiuming, Yue, Jingjing, Nelson, David R., Huang, Lixian, Li, Zhen, Xu, Huimin, Zhou, Dong, Wang, Yongjun, Hu, Weichang, Lin, Jishan, Deng, Youjin, Pandey, Neha, Mancini, Melina, Zerpa, Dessireé, Nguyen, Julie K., Wang, Liming, Xin, Yinghui, Ge, Liangfa, Han, Jennifer O., Chakrabarty, Setu, Pushko, Marija, Zhang, Wenping, Ma, Yanhong, Ma, Panpan, Lv, Mingju, Chen, Faming, Zheng, Guangyong, Xu, Jingsheng, Yang, Zhenhui, Deng, Fang, Chen, Xuequn, Liao, Zhenyang, Zhang, Xunxiao, Lin, Zhicong, Lin, Hai, Yan, Hansong, Kuang, Zheng, Zhong, Weimin, Liang, Pingping, Wang, Guofeng, Yuan, Yuan, Shi, Jiaxian, Hou, Jinxiang, Lin, Jingxian, Jin, Jingjing, Cao, Peijian, Shen, Qiaochu, Jiang, Qing, Zhou, Ping, Ma, Yaying, Zhang, Xiaodan, Xu, Rongrong, Liu, Juan, Zhou, Yongmei, Jia, Haifeng, Ma, Qing, Qi, Rui, Zhang, Zhiliang, Fang, Hongkun, Song, Jinjin, Wang, Mengjuan, Dong, Guangrui, Wang, Gang, Chen, Zheng, Ma, Teng, Liu, Hong, Dhungana, Singha R., Huss, Sarah E., Yang, Xiping, Sharma, Anupma, Trujillo, Jhon H., Martinez, Maria C., Hudson, Matthew, Riascos, John J., Schuler, Mary, Chen, Li-Qing, Braun, David M., Li, Lei, Yu, Qingyi, Wang, Jianping, Wang, Kai, Schatz, Michael C., Heckerman, David, Van Sluys, Marie-Anne, Souza, Glaucia Mendes, Moore, Paul H., Sankoff, David, VanBuren, Robert, Paterson, Andrew H.
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.11.2018; Nature Publishing Group
• Subjects: 09 BIOMASS FUELS; 38/39; 631/208/212; 631/449/2491; Agriculture; Alleles; Animal Genetics and Genomics; Autopolyploidy; BASIC BIOLOGICAL SCIENCES; Binding sites; Biofuels; Bioinformatics; Biomedical and Life Sciences; Biomedicine; Cancer Research; Chromosome number; Chromosome translocations; Chromosomes; Crop diseases; Cultivars; Disease resistance; DNA sequencing; Gene Function; Genes; Genetic aspects; Genomes; Genomics; Homology; Human Genetics; Hybrids; Interspecific; Physiological aspects; Plant Genetics; Polyploidy; Recombination; Saccharum; Saccharum spontaneum; Sugarcane
• ISSN: 1061-4036; 1546-1718
• DOI: 10.1038/s41588-018-0237-2

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. Sequencing of haploid sugarcane, Saccharum spontaneum , allows assembly of a prototypical version of the sugarcane chromosome set. This new reference genome will serve as a resource to accelerate sugarcane improvement.