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The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis
Liu, Jin1,2; Shi, Cong2,3; Shi, Cheng-Cheng4; Li, Wei5; Zhang, Qun-Jie5; Zhang, Yun6; Li, Kui7,8; Lu, Hui-Fang9; Shi, Chao2; Zhu, Si-Tao4; Xiao, Zai-Yun1; Nan, Hong2,3; Yue, Yao4; Zhu, Xun-Ge2,3; Wu, Yu1; Hong, Xiao-Ning4; Fan, Guang-Yi4,9; Tong, Yan2; Zhang, Dan5; Mao, Chang-Li1; Liu, Yun-Long2; Hao, Shi-Jie4; Liu, Wei-Qing9; Lv, Mei-Qi4; Zhang, Hai-Bin2; Liu, Yuan2; Hu-tang, Ge-Ran2,3; Wang, Jin-Peng3,10; Wang, Jia-Hao4; Sun, Ying-Huai9; Ni, Shu-Bang1; Chen, Wen-Bin9; Zhang, Xing-Cai11; Jiao, Yuan-Nian10; Eichler, Evan E.12; Li, Guo-Hua1; Liu, Xin4,9; Gao, Li-Zhi2,5
Corresponding AuthorLiu, Xin(liuxin@genomics.cn) ; Gao, Li-Zhi(lgaogenomics@163.com)
2020-02-03
Source PublicationMOLECULAR PLANT
ISSN1674-2052
Volume13Issue:2Pages:336-350
AbstractThe rubber tree, Hevea brasiliensis, produces natural rubber that serves as an essential industrial raw material. Here, we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing (SMRT) and Hi-C technologies to anchor the similar to 1.47-Gb genome assembly into 18 pseudochromosomes. The chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution, since the common paleopolyploid event occurred before the split of Hevea and Manihot. We show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last 10 million years, leading to the massive expansion by similar to 65.88% (similar to 970 Mbp) of the whole rubber tree genome since the divergence from Manihot. We identify large-scale expansion of genes associated with whole rubber biosynthesis processes, such as basal metabolic processes, ethylene biosynthesis, and the activation of polysaccharide and glycoprotein lectin, which are important properties for latex production. A map of genomic variation between the cultivated and wild rubber trees was obtained, which contains similar to 15.7 million high-quality single-nucleotide polymorphisms. We identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history of rubber tree, some of which are involved in rubber biosynthesis. This genome assembly represents key resources for future rubber tree research and breeding, providing novel targets for improving plant biotic and abiotic tolerance and rubber production.
Keywordrubber tree rubber biosynthesis chromosome evolution whole-genome duplication domestication
DOI10.1016/j.molp.2019.10.017
Indexed BySCI ; SCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Plant Sciences
WOS SubjectBiochemistry & Molecular Biology ; Plant Sciences
WOS IDWOS:000510842700012
Citation statistics
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/70819
Collection中国西南野生生物种质资源库
Corresponding AuthorLiu, Xin; Gao, Li-Zhi
Affiliation1.Yunnan Inst Trop Crops, Jinghong 666100, Peoples R China
2.Chinese Acad Sci, Plant Germplasm & Genom Ctr, Kunming Inst Bot, Germplasm Bank Wild Species Southwestern China, Kunming 650204, Yunnan, Peoples R China
3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
4.BGI Qingdao, Qingdao 266555, Peoples R China
5.South China Agr Univ, Inst Genom & Bioinformat, Guangzhou 510642, Peoples R China
6.Southwest China Forestry Univ, Asia Pacific Trop Forestry Germplasm Inst, Kunming 650224, Yunnan, Peoples R China
7.Nanjing Univ, Sch Life Sci, Nanjing 210023, Peoples R China
8.Novogene Bioinformat Inst, Beijing 100083, Peoples R China
9.BGI Shenzhen, Shenzhen 518083, Peoples R China
10.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China
11.Harvard Univ, John A Paulson Sch Engn & Appl Sci, Cambridge, MA 02138 USA
12.Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA
Recommended Citation
GB/T 7714
Liu, Jin,Shi, Cong,Shi, Cheng-Cheng,et al. The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis[J]. MOLECULAR PLANT,2020,13(2):336-350.
APA Liu, Jin.,Shi, Cong.,Shi, Cheng-Cheng.,Li, Wei.,Zhang, Qun-Jie.,...&Gao, Li-Zhi.(2020).The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis.MOLECULAR PLANT,13(2),336-350.
MLA Liu, Jin,et al."The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis".MOLECULAR PLANT 13.2(2020):336-350.
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