The genome sequence of the orchid Phalaenopsis equestris

被引：359

作者：

Cai, Jing ^{[1
,2
,3
,4
,5
]}

Liu, Xin ^{[6
]}

Vanneste, Kevin ^{[8
]}

Proost, Sebastian ^{[8
]}

Tsai, Wen-Chieh ^{[9
]}

Liu, Ke-Wei ^{[1
,2
,3
,4
,5
]}

Chen, Li-Jun ^{[1
,2
]}

He, Ying ^{[7
,8
]}

Xu, Qing ^{[10
]}

Bian, Chao ^{[6
]}

Zheng, Zhijun ^{[6
]}

Sun, Fengming ^{[6
]}

Liu, Weiqing ^{[6
]}

Hsiao, Yu-Yun ^{[11
]}

Pan, Zhao-Jun ^{[11
]}

Hsu, Chia-Chi ^{[11
]}

Yang, Ya-Ping ^{[11
]}

Hsu, Yi-Chin ^{[11
]}

Chuang, Yu-Chen ^{[11
]}

Dievart, Anne ^{[12
]}

Dufayard, Jean-Francois ^{[12
]}

Xu, Xun ^{[6
]}

Wang, Jun-Yi ^{[6
]}

Wang, Jun ^{[6
]}

Xiao, Xin-Ju ^{[1
,2
]}

Zhao, Xue-Min ^{[13
]}

Du, Rong ^{[13
]}

Zhang, Guo-Qiang ^{[1
,2
]}

Wang, Meina ^{[1
,2
]}

Su, Yong-Yu ^{[14
]}

Xie, Gao-Chang ^{[1
,2
]}

Liu, Guo-Hui ^{[1
,2
]}

Li, Li-Qiang ^{[1
,2
]}

Huang, Lai-Qiang ^{[1
,2
,3
,4
,5
,14
]}

Luo, Yi-Bo ^{[10
]}

Chen, Hong-Hwa ^{[11
,15
]}

Van de Peer, Yves ^{[7
,8
,16
]}

Liu, Zhong-Jian ^{[1
,2
,3
,4
,14
]}

机构：

[1] Natl Orchid Conservat Ctr China, Shenzhen Key Lab Orchid Conservat & Utilizat, Shenzhen, Peoples R China

[2] Orchid Conservat & Res Ctr Shenzhen, Shenzhen, Peoples R China

[3] Tsinghua Univ, Grad Sch Shenzhen, State Key Lab Hlth Sci & Technol, Ctr Biotechnol & BioMed,Shenzhen Key Lab Gene & A, Shenzhen 518057, Peoples R China

[4] Tsinghua Univ, Grad Sch Shenzhen, Div Life & Hlth Sci, Shenzhen 518057, Peoples R China

[5] Tsinghua Univ, Sch Life Sci, Beijing 100084, Peoples R China

[6] BGI Shenzhen, Shenzhen, Peoples R China

[7] VIB, Dept Plant Syst Biol, Ghent, Belgium

[8] Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9000 Ghent, Belgium

[9] Natl Cheng Kung Univ, Inst Trop Plant Sci, Tainan 70101, Taiwan

[10] Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China

[11] Natl Cheng Kung Univ, Dept Life Sci, Tainan 70101, Taiwan

[12] Ctr Cooprat Int Rech Agronom Dev CIRAD, UMR Ameliorat Genet & Adaptat Plantes Mediterrane, Montpellier, France

[13] State Forestry Adm, Beijing, Peoples R China

[14] South China Agr Univ, Coll Forestry, Guangzhou, Guangdong, Peoples R China

[15] Natl Cheng Kung Univ, Orchid Res Ctr, Tainan 70101, Taiwan

[16] Genom Res Inst, Dept Genet, Pretoria, South Africa

来源：

NATURE GENETICS | 2015年 / 47卷 / 01期

基金：

芬兰科学院;

关键词：

CRASSULACEAN ACID METABOLISM; MADS-BOX GENE; MOLECULAR PHYLOGENETICS; PLANT; IDENTIFICATION; DUPLICATIONS; POLYPLOIDY; EPIPHYTISM; EVOLUTION; PROGRAM;

D O I：

10.1038/ng.3149

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers.

引用

页码：65 / +

页数：10

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