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. 2018 Nov;50(11):1565-1573.
doi: 10.1038/s41588-018-0237-2. Epub 2018 Oct 8.

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L

Jisen Zhang  1 , Xingtan Zhang  2 , Haibao Tang  2 , Qing Zhang  2 , Xiuting Hua  2 , Xiaokai Ma  2 , Fan Zhu  3 , Tyler Jones  4 , Xinguang Zhu  5 , John Bowers  6 , Ching Man Wai  7 , Chunfang Zheng  8 , Yan Shi  2 , Shuai Chen  2 , Xiuming Xu  2 , Jingjing Yue  2 , David R Nelson  9 , Lixian Huang  2 , Zhen Li  2 , Huimin Xu  2 , Dong Zhou  2 , Yongjun Wang  2 , Weichang Hu  2 , Jishan Lin  2 , Youjin Deng  2 , Neha Pandey  3 , Melina Mancini  3 , Dessireé Zerpa  3 , Julie K Nguyen  3 , Liming Wang  2 , Liang Yu  3 , Yinghui Xin  3 , Liangfa Ge  3 , Jie Arro  3 , Jennifer O Han  3 , Setu Chakrabarty  3 , Marija Pushko  3 , Wenping Zhang  2 , Yanhong Ma  2 , Panpan Ma  2 , Mingju Lv  5 , Faming Chen  10 , Guangyong Zheng  10 , Jingsheng Xu  2 , Zhenhui Yang  2 , Fang Deng  2 , Xuequn Chen  2 , Zhenyang Liao  2 , Xunxiao Zhang  2 , Zhicong Lin  2 , Hai Lin  2 , Hansong Yan  2 , Zheng Kuang  2 , Weimin Zhong  2 , Pingping Liang  2 , Guofeng Wang  2 , Yuan Yuan  2 , Jiaxian Shi  2 , Jinxiang Hou  2 , Jingxian Lin  2 , Jingjing Jin  11 , Peijian Cao  11 , Qiaochu Shen  2 , Qing Jiang  2 , Ping Zhou  2 , Yaying Ma  2 , Xiaodan Zhang  2 , Rongrong Xu  2 , Juan Liu  2 , Yongmei Zhou  2 , Haifeng Jia  2 , Qing Ma  2 , Rui Qi  2 , Zhiliang Zhang  2 , Jingping Fang  2 , Hongkun Fang  2 , Jinjin Song  2 , Mengjuan Wang  2 , Guangrui Dong  2 , Gang Wang  2 , Zheng Chen  2 , Teng Ma  2 , Hong Liu  2 , Singha R Dhungana  12 , Sarah E Huss  3 , Xiping Yang  13 , Anupma Sharma  14 , Jhon H Trujillo  15 , Maria C Martinez  15 , Matthew Hudson  16 , John J Riascos  15 , Mary Schuler  3 , Li-Qing Chen  3 , David M Braun  12 , Lei Li  2 , Qingyi Yu  14 , Jianping Wang  2   13 , Kai Wang  2 , Michael C Schatz  17 , David Heckerman  18 , Marie-Anne Van Sluys  19 , Glaucia Mendes Souza  20 , Paul H Moore  4 , David Sankoff  8 , Robert VanBuren  7 , Andrew H Paterson  6 , Chifumi Nagai  21 , Ray Ming  22   23
Affiliations

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L

Jisen Zhang et al. Nat Genet. 2018 Nov.

Erratum in

  • Publisher Correction: Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.
    Zhang J, Zhang X, Tang H, Zhang Q, Hua X, Ma X, Zhu F, Jones T, Zhu X, Bowers J, Wai CM, Zheng C, Shi Y, Chen S, Xu X, Yue J, Nelson DR, Huang L, Li Z, Xu H, Zhou D, Wang Y, Hu W, Lin J, Deng Y, Pandey N, Mancini M, Zerpa D, Nguyen JK, Wang L, Yu L, Xin Y, Ge L, Arro J, Han JO, Chakrabarty S, Pushko M, Zhang W, Ma Y, Ma P, Lv M, Chen F, Zheng G, Xu J, Yang Z, Deng F, Chen X, Liao Z, Zhang X, Lin Z, Lin H, Yan H, Kuang Z, Zhong W, Liang P, Wang G, Yuan Y, Shi J, Hou J, Lin J, Jin J, Cao P, Shen Q, Jiang Q, Zhou P, Ma Y, Zhang X, Xu R, Liu J, Zhou Y, Jia H, Ma Q, Qi R, Zhang Z, Fang J, Fang H, Song J, Wang M, Dong G, Wang G, Chen Z, Ma T, Liu H, Dhungana SR, Huss SE, Yang X, Sharma A, Trujillo JH, Martinez MC, Hudson M, Riascos JJ, Schuler M, Chen LQ, Braun DM, Li L, Yu Q, Wang J, Wang K, Schatz MC, Heckerman D, Van Sluys MA, Souza GM, Moore PH, Sankoff D, VanBuren R, Paterson AH, Nagai C, Ming R. Zhang J, et al. Nat Genet. 2018 Dec;50(12):1754. doi: 10.1038/s41588-018-0293-7. Nat Genet. 2018. PMID: 30425353

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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