A genome for gnetophytes and early evolution of seed plants

doi:10.1038/s41477-017-0097-2

	A genome for gnetophytes and early evolution of seed plants
	Wan, Tao ; Liu, Zhi-Ming ; Li, Ling-Fei ; Leitch, Andrew R.; Leitch, Ilia J.; Lohaus, Rolf 5,6; Liu, Zhong-Jian ; Xin, Hai-Ping ; Gong, Yan-Bing ; Liu, Yang ; Wang, Wen-Cai ; Chen, Ling-Yun ; Yang, Yong 12; Kelly, Laura J.; Yang, Ji 13; Huang, Jin-Ling ; Li, Zhen 5,6; Liu, Ping ; Zhang, Li ; Liu, Hong-Mei ; Wang, Hui ; Deng, Shu-Han ; Liu, Meng ; Li, Ji ; Ma, Lu 3; Liu, Yan ; Lei, Yang ; Xu, Wei ; Wu, Ling-Qing ; Liu, Fan ; Ma, Qian 10; Yu, Xin-Ran ; Jiang, Zhi ; Zhang, Guo-Qiang ; Li, Shao-Hua; Li, Rui-Qiang ; Zhang, Shou-Zhou ; Wang, Qing-Feng ; Van de Peer, Yves 5,6,17; Zhang, Jin-Bo ; Wang, Xiao-Ming
	2018
发表期刊	NATURE PLANTS
ISSN	2055-026X
卷号	4 期号:2 页码:82-89
摘要	Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel genome assembly strategy to deal with high levels of heterozygosity, we assembled >4 Gb of sequence encoding 27,491 protein-coding genes. Comparative analysis of the G. montanum genome with other gymnosperm genomes unveiled some remarkable and distinctive genomic features, such as a diverse assemblage of retrotransposons with evidence for elevated frequencies of elimination rather than accumulation, considerable differences in intron architecture, including both length distribution and proportions of (retro) transposon elements, and distinctive patterns of proliferation of functional protein domains. Furthermore, a few gene families showed Gnetum-specific copy number expansions (for example, cellulose synthase) or contractions (for example, Late Embryogenesis Abundant protein), which could be connected with Gnetum's distinctive morphological innovations associated with their adaptation to warm, mesic environments. Overall, the G. montanum genome enables a better resolution of ancestral genomic features within seed plants, and the identification of genomic characters that distinguish Gnetum from other gymnosperms.
学科领域	Plant Sciences
DOI	10.1038/s41477-017-0097-2
收录类别	SCI
语种	英语
WOS关键词	GENE FAMILY ; COLD STRESS ; ORIGIN ; SEQUENCE ; ANGIOSPERMS ; POLYPLOIDY ; EXPRESSION ; PHYLOGENY ; DIVERSITY ; SIZE
WOS记录号	WOS:000425119600012
出版者	NATURE PUBLISHING GROUP
文献子类	Article
出版地	LONDON
EISSN	2055-0278
资助机构	Novogene Bioinformatics Institute, Beijing, China [NHT140016, NVT140016004] ; Scientific Project of Shenzhen Urban Administration [201519] ; Innovation of Science and Technology Commission of Shenzhen [JSGG20140515164852417] ; Sino-Africa Joint Research Center [SAJL201607] ; Ghent UniversityGhent University [01MR0310W] ; European Union Seventh Framework Programme under European Research Council [322739-DOUBLEUP]
作者邮箱	qfwang@wbgcas.cn ; yves.vandepeer@psb.vib-ugent.be ; zhangjinbo@novogene.com ; 719921868@qq.com
作品OA属性	Green Published, hybrid, Green Submitted
引用统计	被引频次：122[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/20437
专题	系统与进化植物学国家重点实验室
作者单位	1.Shenzhen & Chinese Acad Sci, Fairy Lake Bot Garden, Key Lab Southern Subtrop Plant Divers, Shenzhen, Peoples R China 2.Chinese Acad Sci, Sinoafrica Joint Res Ctr, Wuhan, Hubei, Peoples R China 3.Novogene Bioinformat Inst, Beijing, Peoples R China 4.Queen Mary Univ London, Sch Biol & Chem Sci, London, England 5.Leitch, Ilia J.] Royal Bot Gardens, Jodrell Lab, Richmond, England 6.Univ Ghent, Dept Plant Biotechnol & Bioinformat, Ghent, Belgium 7.Ctr Plant Syst Biol VIB, Ghent, Belgium 8.Natl Orchid Conservat Ctr China, Shenzhen Key Lab Orchid Conservat & Utilizat, Shenzhen, Peoples R China 9.Orchid Conservat & Res Ctr, Shenzhen, Peoples R China 10.Chinese Acad Sci, Wuhan Bot Garden, Key Lab Plant Germplasm Enhancement & Specialty A, Wuhan, Hubei, Peoples R China 11.Wuhan Univ, Coll Life Sci, State Key Lab Hybrid Rice, Wuhan, Hubei, Peoples R China 12.Chinese Acad Sci, Wuhan Bot Garden, Key Lab Aquat Bot & Watershed Ecol, Wuhan, Hubei, Peoples R China 13.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 14.Fudan Univ, Educ Key Lab Biodivers Sci & Ecol Engn, Shanghai, Peoples R China 15.Henan Univ, State Key Lab Cotton Biol, Inst Plant Stress Biol, Kaifeng, Peoples R China 16.East Carolina Univ, Dept Biol, Greenville, NC USA 17.Chinese Acad Sci, Inst Bot, Beijing Key Lab Grape Sci & Enol, Beijing, Peoples R China 18.Univ Pretoria, Genom Res Inst, Pretoria, South Africa
推荐引用方式 GB/T 7714	Wan, Tao,Liu, Zhi-Ming,Li, Ling-Fei,et al. A genome for gnetophytes and early evolution of seed plants[J]. NATURE PLANTS,2018,4(2):82-89.
APA	Wan, Tao.,Liu, Zhi-Ming.,Li, Ling-Fei.,Leitch, Andrew R..,Leitch, Ilia J..,...&Wang, Xiao-Ming.(2018).A genome for gnetophytes and early evolution of seed plants.NATURE PLANTS,4(2),82-89.
MLA	Wan, Tao,et al."A genome for gnetophytes and early evolution of seed plants".NATURE PLANTS 4.2(2018):82-89.

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