The Apostasia genome and the evolution of orchids

doi:10.1016/j.syapm.2016.12.003

	The Apostasia genome and the evolution of orchids
	Zhang, Guo-Qiang ; Liu, Ke-Wei ; Li, Zhen ; Lohaus, Rolf ; Hsiao, Yu-Yun ; Niu, Shan-Ce ; Wang, Jie-Yu ; Lin, Yao-Cheng ; Xu, Qing ; Chen, Li-Jun ; Yoshida, Kouki 8; Fujiwara, Sumire ; Wang, Zhi-Wen ; Zhang, Yong-Qiang ; Mitsuda, Nobutaka ; Wang, Meina ; Liu, Guo-Hui ; Pecoraro, Lorenzo ; Huang, Hui-Xia ; Xiao, Xin-Ju ; Lin, Min ; Wu, Xin-Yi ; Wu, Wan-Lin ; Chen, You-Yi ; Chang, Song-Bin ; Sakamoto, Shingo ; Ohme-Takagi, Masaru ; Yagi, Masafumi 12; Zeng, Si-Jin ; Shen, Ching-Yu ; Yeh, Chuan-Ming ; Luo, Yi-Bo; Tsai, Wen-Chieh ; Van de Peer, Yves 2,3,14; Liu, Zhong-Jian
	2017
发表期刊	NATURE
ISSN	0028-0836
卷号	549 期号:7672 页码:379+
摘要	Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth(1-3). Here we report the draft genome sequence of Apostasia shenzhenica(4), a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.
学科领域	Biotechnology & Applied Microbiology ; Microbiology
DOI	10.1016/j.syapm.2016.12.003
收录类别	SCI
语种	英语
WOS关键词	MADS-BOX GENES ; MULTIPLE SEQUENCE ALIGNMENT ; PHYLOGENETIC ANALYSIS ; MAXIMUM-LIKELIHOOD ; SUPPLEMENT TREMBL ; NEW-JERSEY ; ARABIDOPSIS ; INFERENCE ; ORIGIN ; SCALE
WOS记录号	WOS:000395610300006
出版者	NATURE PORTFOLIO
文献子类	Article
出版地	BERLIN
EISSN	1476-4687
资助机构	Funds for Environmental Project of Shenzhen, China [2013-02] ; State Forestry Administration P. R. China [2011-4-53] ; Funds for Forestry Science and Technology Innovation Project of Guangdong, China [2016KJCX025, 2013KJCX014-05] ; Fundamental Research Project of Shenzhen, China [JCYJ20170307170746099, JCYJ20150403150235943] ; Guangdong Natural Science FoundationNational Natural Science Foundation of Guangdong Province [2017A030312004] ; Multidisciplinary Research Partnership 'Bioinformatics: from nucleotides to networks' Project of Ghent University [01MR0310W] ; European Union under European Research Council [322739-DOUBLEUP]
作者邮箱	cmyeh@mail.saitama-u.ac.jp ; luoyb@ibcas.ac.cn ; tsaiwc@mail.ncku.edu.tw ; yves.vandepeer@psb.vib-ugent.be ; liuzj@sinicaorchid.org
引用统计	被引频次：28[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/2S10CLM1/22143
专题	系统与进化植物学国家重点实验室
作者单位	1.Natl Orchid Conservat Ctr China, Shenzhen Key Lab Orchid Conservat & Utilizat, Shenzhen 518114, Peoples R China 2.Orchid Conservat & Res Ctr Shenzhen, Shenzhen 518114, Peoples R China 3.Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9052 Ghent, Belgium 4.VIB Ctr Plant Syst Biol, B-9052 Ghent, Belgium 5.Natl Cheng Kung Univ, Orchid Res & Dev Ctr, Tainan 701, Taiwan 6.Natl Cheng Kung Univ, Dept Life Sci, Tainan 701, Taiwan 7.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 8.South China Agr Univ, Coll Forestry, Guangzhou 510640, Guangdong, Peoples R China 9.Taisei Corp, Technol Ctr, Totsuka Ku, Nase Cho 344-1, Yokohama, Kanagawa 2450051, Japan 10.Natl Inst Adv Ind Sci & Technol, Bioprod Res Inst, Cent 6,Higashi 1-1-1, Tsukuba, Ibaraki 3058562, Japan 11.PubBiotech Serv Corp, Wuhan 430070, Hubei, Peoples R China 12.Saitama Univ, Grad Sch Sci & Engn, Sakura Ku, 255 Shimo Okubo, Saitama 3388570, Japan 13.NIFS, 2-1 Fujimoto, Tsukuba, Ibaraki 3058519, Japan 14.Natl Cheng Kung Univ, Inst Trop Plant Sci, Tainan 701, Taiwan 15.Genom Res Inst, Dept Genet, ZA-0028 Pretoria, South Africa 16.Fujian Agr & Forestry Univ, Coll Landscape Architecture, Fuzhou 350002, Fujian, Peoples R China 17.Tsinghua Univ, Grad Sch Shenzhen, Ctr Biotechnol & BioMed, Shenzhen 518055, Peoples R China 18.Acad Sinica, Biotechnol Ctr Southern Taiwan, Agr Biotechnol Res Ctr, Tainan 741, Taiwan
推荐引用方式 GB/T 7714	Zhang, Guo-Qiang,Liu, Ke-Wei,Li, Zhen,et al. The Apostasia genome and the evolution of orchids[J]. NATURE,2017,549(7672):379+.
APA	Zhang, Guo-Qiang.,Liu, Ke-Wei.,Li, Zhen.,Lohaus, Rolf.,Hsiao, Yu-Yun.,...&Liu, Zhong-Jian.(2017).The Apostasia genome and the evolution of orchids.NATURE,549(7672),379+.
MLA	Zhang, Guo-Qiang,et al."The Apostasia genome and the evolution of orchids".NATURE 549.7672(2017):379+.

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