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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Author(s):
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Zhang, Jisen [1] ; Zhang, Xingtan [1] ; Tang, Haibao [1] ; Zhang, Qing [1] ; Hua, Xiuting [1] ; Ma, Xiaokai [1] ; Zhu, Fan [2] ; Jones, Tyler [3] ; Zhu, Xinguang [4] ; Bowers, John [5] ; Wai, Ching Man [6] ; Zheng, Chunfang [7] ; Shil, Yan [1] ; Chen, Shuai [1] ; Xu, Xiuming [1] ; Yue, Jingjing [1] ; Nelsons, David R. [8] ; Huang, Lixian [1] ; Li, Zhen [1] ; Xu, Huimin [1] ; Zhou, Dong [1] ; Wang, Yongjun [1] ; Hu, Weichang [1] ; Lin, Jishan [1] ; Deng, Youjin [1] ; Pandey, Neha [2] ; Mancini, Melina [2] ; Zerpa, Dessiree [2] ; Nguyen, Julie K. [2] ; Wang, Liming [1] ; Yu, Liang [2] ; Xin, Yinghui [2] ; Ge, Liangfa [2] ; Arro, Jie [2] ; Han, Jennifer O. [2] ; Chakrabarty, Setu [2] ; Pushko, Marija [2] ; Zhang, Wenping [1] ; Ma, Yanhong [1] ; Ma, Panpan [1] ; Lv, Mingju [4] ; Chen, Faming [9] ; Zheng, Guangyong [9] ; Xu, Jingsheng [1] ; Yang, Zhenhui [1] ; Deng, Fang [1] ; Chen, Xuequn [1] ; Liao, Zhenyang [1] ; Zhang, Xunxiao [1] ; Lin, Zhicong [1] ; Lin, Hai [1] ; Yan, Hansong [1] ; Kuang, Zheng [1] ; Zhong, Weimin [1] ; Liang, Pingping [1] ; Wang, Guofeng [1] ; Yuan, Yuan [1] ; Shi, Jiaxian [1] ; Hou, Jinxiang [1] ; Lin, Jingxian [1] ; Jin, Jingjing [10] ; Cao, Peijian [10] ; Shen, Qiaochu [1] ; Jiang, Qing [1] ; Zhou, Ping [1] ; Ma, Yaying [1] ; Zhang, Xiaodan [1] ; Xu, Rongrong [1] ; Liu, Juan [1] ; Zhou, Yongmei [1] ; Jia, Haifeng [1] ; Ma, Qing [1] ; Qi, Rui [1] ; Zhang, Zhiliang [1] ; Fang, Jingping [1] ; Fang, Hongkun [1] ; Song, Jinjin [1] ; Wang, Mengjuan [1] ; Dong, Guangrui [1] ; Wang, Gang [1] ; Chen, Zheng [1] ; Ma, Teng [1] ; Liu, Hong [1] ; Dhungana, Singha R. [11] ; Huss, Sarah E. [2] ; Yang, Xiping [12] ; Sharma, Anupma [13] ; Trujillo, Jhon H. [14] ; Martinez, Maria C. [14] ; Hudson, Matthew [15] ; Riascos, John J. [14] ; Schuler, Mary [2] ; Chen, Li-Qing [2] ; Braun, David M. [11] ; Li, Lei [1] ; Yu, Qingyi [13] ; Wang, Jianping [12, 1] ; Wang, Kai [1] ; Schatz, Michael C. [16, 17] ; Heckerman, David [18] ; Van Sluys, Marie-Anne [19] ; Souza, Glaucia Mendes [20] ; Moore, Paul H. [3] ; Sankoff, David [7] ; VanBuren, Robert [6] ; Paterson, Andrew H. [5] ; Nagai, Chifumi [3] ; Ming, Ray [2, 1]
Total Authors: 108
Affiliation:
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[1] Fujian Agr & Forestry Univ, Minist Educ, Fujian Prov Key Lab Haixia Appl Plant, Key Lab Genet Breeding & Multiple Utilizat Corps, Natl Sugarcane Engn Technol Res Ctr, Fujian Agr &, Fuzhou, Fujian - Peoples R China
[2] Univ Illinois, Dept Plant Biol, Urbana, IL 61801 - USA
[3] Hawaii Agr Res Ctr, Kunia, HI 96759 - USA
[4] Chinese Acad Sci, Inst Plant Physiol & Ecol, Shanghai - Peoples R China
[5] Univ Georgia, Dept Plant Biol, Athens, GA 30602 - USA
[6] Michigan State Univ, Dept Hort, E Lansing, MI 48824 - USA
[7] Univ Ottawa, Dept Math & Stat, Ottawa, ON - Canada
[8] Univ Tennessee HSC, Dept Microbiol Immunol & Biochem, Memphis, TN - USA
[9] Chinese Acad Sci, Chinese Acad Sci Max Planck Gesell Partner Inst C, Shanghai - Peoples R China
[10] CNTC, Zhengzhou Tobacco Res Inst, China Tobacco Gene Res Ctr, Zhengzhou, Henan - Peoples R China
[11] Univ Missouri, Div Biol Sci, Columbia, MO 65211 - USA
[12] Univ Florida, Dept Agron, Gainesville, FL 32611 - USA
[13] Texas A&M Univ Syst, Texas A&M AgriLife Res, Dallas, TX - USA
[14] Ctr Invest Cana Azucar Colombia Cenicana, Cali - Colombia
[15] Univ Illinois, Dept Crop Sci, Urbana, IL - USA
[16] Johns Hopkins Univ, Dept Biol, Baltimore, MD 21218 - USA
[17] Johns Hopkins Univ, Dept Comp Sci, Baltimore, MD 21218 - USA
[18] Microsoft Res, Redmond, WA - USA
[19] Univ Sao Paulo, Inst Biociencias, Dept Bot, Sao Paulo - Brazil
[20] Univ Sao Paulo, Dept Bioquim, Inst Quim, Sao Paulo - Brazil
Total Affiliations: 20
Document type: Journal article
Source: Nature Genetics; v. 50, n. 11, p. 1565+, NOV 2018.
Web of Science Citations: 37
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. (AU)

FAPESP's process: 14/50921-8 - Signaling and regulatory network studies associated to the energy cane
Grantee:Glaucia Mendes Souza
Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants
FAPESP's process: 12/51062-3 - Development of an algorithm for the assembly of the sugarcane polyploid genome
Grantee:Glaucia Mendes Souza
Support Opportunities: Program for Research on Bioenergy (BIOEN) - Research Partnership for Technological Innovation (PITE)
FAPESP's process: 08/52146-0 - Sugarcane signaling and regulatory networks
Grantee:Glaucia Mendes Souza
Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants