Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Jisen Zhang, Xingtan Zhang, Haibao Tang, Qing Zhang, Xiuting Hua, Xiaokai Ma, Fan Zhu, Tyler Jones, Xinguang Zhu, John Bowers, Ching Man Wai, Chunfang Zheng, Yan Shi, Shuai Chen, Xiuming Xu, Jingjing Yue, David Nelson, Lixian Huang, Zhen Li, Huimin Xu & 88 others Dong Zhou, Yongjun Wang, Weichang Hu, Jishan Lin, Youjin Deng, Neha Pandey, Melina Mancini, Dessireé Zerpa, Julie K. Nguyen, Liming Wang, Liang Yu, Yinghui Xin, Liangfa Ge, Jie Arro, Jennifer O. Han, Setu Chakrabarty, Marija Pushko, Wenping Zhang, Yanhong Ma, Panpan Ma, Mingju Lv, Faming Chen, Guangyong Zheng, Jingsheng Xu, Zhenhui Yang, Fang Deng, Xuequn Chen, Zhenyang Liao, Xunxiao Zhang, Zhicong Lin, Hai Lin, Hansong Yan, Zheng Kuang, Weimin Zhong, Pingping Liang, Guofeng Wang, Yuan Yuan, Jiaxian Shi, Jinxiang Hou, Jingxian Lin, Jingjing Jin, Peijian Cao, Qiaochu Shen, Qing Jiang, Ping Zhou, Yaying Ma, Xiaodan Zhang, Rongrong Xu, Juan Liu, Yongmei Zhou, Haifeng Jia, Qing Ma, Rui Qi, Zhiliang Zhang, Jingping Fang, Hongkun Fang, Jinjin Song, Mengjuan Wang, Guangrui Dong, Gang Wang, Zheng Chen, Teng Ma, Hong Liu, Singha R. Dhungana, Sarah E. Huss, Xiping Yang, Anupma Sharma, Jhon H. Trujillo, Maria C. Martinez, Matthew Hudson, John J. Riascos, Mary Schuler, Li Qing Chen, David M. Braun, Lei Li, Qingyi Yu, Jianping Wang, Kai Wang, Michael C. Schatz, David Heckerman, Marie Anne Van Sluys, Glaucia Mendes Souza, Paul H. Moore, David Sankoff, Robert VanBuren, Andrew H. Paterson, Chifumi Nagai, Ray Ming

Research output: Contribution to journalArticle

17 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1565-1573
Number of pages9
JournalNature Genetics
Volume50
Issue number11
DOIs
StatePublished - Nov 1 2018

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Saccharum
Alleles
Genome
Chromosomes, Human, Pair 4
Disease Resistance
Chromosomes, Human, Pair 8
Chromosomes, Human, Pair 10
Polyploidy
Chromosomes, Human, Pair 2
Haploidy
Genetic Recombination
Genes
Nucleotides
Chromosomes
Binding Sites

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Zhang, J., Zhang, X., Tang, H., Zhang, Q., Hua, X., Ma, X., ... Ming, R. (2018). Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nature Genetics, 50(11), 1565-1573. https://doi.org/10.1038/s41588-018-0237-2

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. / Zhang, Jisen; Zhang, Xingtan; Tang, Haibao; Zhang, Qing; Hua, Xiuting; Ma, Xiaokai; Zhu, Fan; Jones, Tyler; Zhu, Xinguang; Bowers, John; Wai, Ching Man; Zheng, Chunfang; Shi, Yan; Chen, Shuai; Xu, Xiuming; Yue, Jingjing; Nelson, David; 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; Yu, Liang; Xin, Yinghui; Ge, Liangfa; Arro, Jie; 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, Jingping; 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.; Nagai, Chifumi; Ming, Ray.

In: Nature Genetics, Vol. 50, No. 11, 01.11.2018, p. 1565-1573.

Research output: Contribution to journalArticle

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, D, 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 2018, 'Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.', Nature Genetics, vol. 50, no. 11, pp. 1565-1573. https://doi.org/10.1038/s41588-018-0237-2
Zhang, Jisen ; Zhang, Xingtan ; Tang, Haibao ; Zhang, Qing ; Hua, Xiuting ; Ma, Xiaokai ; Zhu, Fan ; Jones, Tyler ; Zhu, Xinguang ; Bowers, John ; Wai, Ching Man ; Zheng, Chunfang ; Shi, Yan ; Chen, Shuai ; Xu, Xiuming ; Yue, Jingjing ; Nelson, David ; 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 ; Yu, Liang ; Xin, Yinghui ; Ge, Liangfa ; Arro, Jie ; 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, Jingping ; 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. ; Nagai, Chifumi ; Ming, Ray. / Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. In: Nature Genetics. 2018 ; Vol. 50, No. 11. pp. 1565-1573.
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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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T1 - Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

AU - Zhang, Jisen

AU - Zhang, Xingtan

AU - Tang, Haibao

AU - Zhang, Qing

AU - Hua, Xiuting

AU - Ma, Xiaokai

AU - Zhu, Fan

AU - Jones, Tyler

AU - Zhu, Xinguang

AU - Bowers, John

AU - Wai, Ching Man

AU - Zheng, Chunfang

AU - Shi, Yan

AU - Chen, Shuai

AU - Xu, Xiuming

AU - Yue, Jingjing

AU - Nelson, David

AU - Huang, Lixian

AU - Li, Zhen

AU - Xu, Huimin

AU - Zhou, Dong

AU - Wang, Yongjun

AU - Hu, Weichang

AU - Lin, Jishan

AU - Deng, Youjin

AU - Pandey, Neha

AU - Mancini, Melina

AU - Zerpa, Dessireé

AU - Nguyen, Julie K.

AU - Wang, Liming

AU - Yu, Liang

AU - Xin, Yinghui

AU - Ge, Liangfa

AU - Arro, Jie

AU - Han, Jennifer O.

AU - Chakrabarty, Setu

AU - Pushko, Marija

AU - Zhang, Wenping

AU - Ma, Yanhong

AU - Ma, Panpan

AU - Lv, Mingju

AU - Chen, Faming

AU - Zheng, Guangyong

AU - Xu, Jingsheng

AU - Yang, Zhenhui

AU - Deng, Fang

AU - Chen, Xuequn

AU - Liao, Zhenyang

AU - Zhang, Xunxiao

AU - Lin, Zhicong

AU - Lin, Hai

AU - Yan, Hansong

AU - Kuang, Zheng

AU - Zhong, Weimin

AU - Liang, Pingping

AU - Wang, Guofeng

AU - Yuan, Yuan

AU - Shi, Jiaxian

AU - Hou, Jinxiang

AU - Lin, Jingxian

AU - Jin, Jingjing

AU - Cao, Peijian

AU - Shen, Qiaochu

AU - Jiang, Qing

AU - Zhou, Ping

AU - Ma, Yaying

AU - Zhang, Xiaodan

AU - Xu, Rongrong

AU - Liu, Juan

AU - Zhou, Yongmei

AU - Jia, Haifeng

AU - Ma, Qing

AU - Qi, Rui

AU - Zhang, Zhiliang

AU - Fang, Jingping

AU - Fang, Hongkun

AU - Song, Jinjin

AU - Wang, Mengjuan

AU - Dong, Guangrui

AU - Wang, Gang

AU - Chen, Zheng

AU - Ma, Teng

AU - Liu, Hong

AU - Dhungana, Singha R.

AU - Huss, Sarah E.

AU - Yang, Xiping

AU - Sharma, Anupma

AU - Trujillo, Jhon H.

AU - Martinez, Maria C.

AU - Hudson, Matthew

AU - Riascos, John J.

AU - Schuler, Mary

AU - Chen, Li Qing

AU - Braun, David M.

AU - Li, Lei

AU - Yu, Qingyi

AU - Wang, Jianping

AU - Wang, Kai

AU - Schatz, Michael C.

AU - Heckerman, David

AU - Van Sluys, Marie Anne

AU - Souza, Glaucia Mendes

AU - Moore, Paul H.

AU - Sankoff, David

AU - VanBuren, Robert

AU - Paterson, Andrew H.

AU - Nagai, Chifumi

AU - Ming, Ray

PY - 2018/11/1

Y1 - 2018/11/1

N2 - 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.

AB - 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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