title: The genome sequence of the orchid Phalaenopsis equestris.
abstract: 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.
authors.affiliation: 1] Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China. [2] Center for Biotechnology and BioMedicine, Shenzhen Key Laboratory of Gene &Antibody Therapy, State Key Laboratory of Health Science &Technology (prep) and Division of Life &Health Sciences, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China. [3] School of Life Science, Tsinghua University, Beijing, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Cai
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: 1] Department of Plant Systems Biology, VIB, Ghent, Belgium. [2] Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
authors.forename: Kevin
authors.initials: K
authors.lastname: Vanneste
authors.affiliation: 1] Department of Plant Systems Biology, VIB, Ghent, Belgium. [2] Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Proost
authors.affiliation: Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Wen-Chieh
authors.initials: WC
authors.lastname: Tsai
authors.affiliation: 1] Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China. [2] Center for Biotechnology and BioMedicine, Shenzhen Key Laboratory of Gene &Antibody Therapy, State Key Laboratory of Health Science &Technology (prep) and Division of Life &Health Sciences, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China. [3] School of Life Science, Tsinghua University, Beijing, China.
authors.forename: Ke-Wei
authors.initials: KW
authors.lastname: Liu
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China.
authors.forename: Li-Jun
authors.initials: LJ
authors.lastname: Chen
authors.affiliation: 1] Department of Plant Systems Biology, VIB, Ghent, Belgium. [2] Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
authors.forename: Ying
authors.initials: Y
authors.lastname: He
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Xu
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Chao
authors.identifier: 000000019904721X
authors.initials: C
authors.lastname: Bian
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Zhijun
authors.initials: Z
authors.lastname: Zheng
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Fengming
authors.initials: F
authors.lastname: Sun
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Weiqing
authors.initials: W
authors.lastname: Liu
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Yu-Yun
authors.initials: YY
authors.lastname: Hsiao
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Zhao-Jun
authors.initials: ZJ
authors.lastname: Pan
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Chia-Chi
authors.initials: CC
authors.lastname: Hsu
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Ya-Ping
authors.initials: YP
authors.lastname: Yang
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Yi-Chin
authors.initials: YC
authors.lastname: Hsu
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Yu-Chen
authors.initials: YC
authors.lastname: Chuang
authors.affiliation: Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Montpellier, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Dievart
authors.affiliation: Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Montpellier, France.
authors.forename: Jean-Francois
authors.initials: JF
authors.lastname: Dufayard
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Jun-Yi
authors.initials: JY
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China.
authors.forename: Xin-Ju
authors.initials: XJ
authors.lastname: Xiao
authors.affiliation: State Forestry Administration, Beijing, China.
authors.forename: Xue-Min
authors.initials: XM
authors.lastname: Zhao
authors.affiliation: State Forestry Administration, Beijing, China.
authors.forename: Rong
authors.initials: R
authors.lastname: Du
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China.
authors.forename: Guo-Qiang
authors.initials: GQ
authors.lastname: Zhang
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China.
authors.forename: Meina
authors.initials: M
authors.lastname: Wang
authors.affiliation: College of Forestry, South China Agriculture University, Guangzhou, China.
authors.forename: Yong-Yu
authors.initials: YY
authors.lastname: Su
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China.
authors.forename: Gao-Chang
authors.initials: GC
authors.lastname: Xie
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China.
authors.forename: Guo-Hui
authors.initials: GH
authors.lastname: Liu
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China.
authors.forename: Li-Qiang
authors.initials: LQ
authors.lastname: Li
authors.affiliation: 1] Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China. [2] Center for Biotechnology and BioMedicine, Shenzhen Key Laboratory of Gene &Antibody Therapy, State Key Laboratory of Health Science &Technology (prep) and Division of Life &Health Sciences, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China. [3] School of Life Science, Tsinghua University, Beijing, China. [4] College of Forestry, South China Agriculture University, Guangzhou, China.
authors.forename: Lai-Qiang
authors.initials: LQ
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yi-Bo
authors.initials: YB
authors.lastname: Luo
authors.affiliation: 1] Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan. [2] Orchid Research Center, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Hong-Hwa
authors.initials: HH
authors.lastname: Chen
authors.affiliation: 1] Department of Plant Systems Biology, VIB, Ghent, Belgium. [2] Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. [3] Department of Genetics, Genomics Research Institute, Pretoria, South Africa.
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.affiliation: 1] Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China. [2] Center for Biotechnology and BioMedicine, Shenzhen Key Laboratory of Gene &Antibody Therapy, State Key Laboratory of Health Science &Technology (prep) and Division of Life &Health Sciences, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China. [3] College of Forestry, South China Agriculture University, Guangzhou, China.
authors.forename: Zhong-Jian
authors.identifier: 0000000343903878
authors.initials: ZJ
authors.lastname: Liu
mesh_terms: D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D007438:Introns / Q000235:genetics; D026161:MADS Domain Proteins; D059645:Mutation Rate; D029595:Orchidaceae / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D010788:Photosynthesis / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D018749:RNA, Plant / Q000096:biosynthesis / Q000235:genetics; D016415:Sequence Alignment; D013045:Species Specificity
chemical_list: D026161:MADS Domain Proteins; D010940:Plant Proteins; D012333:RNA, Messenger; D018749:RNA, Plant