title: The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution.
abstract: Orchids make up about 10% of all seed plant species, have great economical value, and are of specific scientific interest because of their renowned flowers and ecological adaptations. Here, we report the first draft genome sequence of a lithophytic orchid, Dendrobium catenatum. We predict 28,910 protein-coding genes, and find evidence of a whole genome duplication shared with Phalaenopsis. We observed the expansion of many resistance-related genes, suggesting a powerful immune system responsible for adaptation to a wide range of ecological niches. We also discovered extensive duplication of genes involved in glucomannan synthase activities, likely related to the synthesis of medicinal polysaccharides. Expansion of MADS-box gene clades ANR1, StMADS11, and MIKC(*), involved in the regulation of development and growth, suggests that these expansions are associated with the astonishing diversity of plant architecture in the genus Dendrobium. On the contrary, members of the type I MADS box gene family are missing, which might explain the loss of the endospermous seed. The findings reported here will be important for future studies into polysaccharide synthesis, adaptations to diverse environments and flower architecture of Orchidaceae.
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.
authors.forename: Guo-Qiang
authors.initials: GQ
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Xu
authors.affiliation: Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen 518083, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Bian
authors.affiliation: Dapartment of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.|Orchid Research Center, National Cheng Kung University, Tainan 701, Taiwan.|Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Wen-Chieh
authors.initials: WC
authors.lastname: Tsai
authors.affiliation: Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan.
authors.forename: Chuan-Ming
authors.initials: CM
authors.lastname: Yeh
authors.affiliation: The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China.
authors.forename: Ke-Wei
authors.initials: KW
authors.lastname: Liu
authors.affiliation: Technology Center, Taisei Corporation, Kanagawa 245-0051, Japan.
authors.forename: Kouki
authors.initials: K
authors.lastname: Yoshida
authors.affiliation: Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
authors.forename: Liang-Sheng
authors.initials: LS
authors.lastname: Zhang
authors.affiliation: Dapartment of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Song-Bin
authors.initials: SB
authors.lastname: Chang
authors.affiliation: Fruit Crop Systems Biology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Chen
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.|College of Forestry, South China Agricultural University, Guangzhou, 510640, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Shi
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.|College of Forestry, South China Agricultural University, Guangzhou, 510640, China.
authors.forename: Yong-Yu
authors.initials: YY
authors.lastname: Su
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.
authors.forename: Yong-Qiang
authors.initials: YQ
authors.lastname: Zhang
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.
authors.forename: Li-Jun
authors.initials: LJ
authors.lastname: Chen
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.
authors.forename: Yayi
authors.initials: Y
authors.lastname: Yin
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.
authors.forename: Min
authors.initials: M
authors.lastname: Lin
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.
authors.forename: Huixia
authors.initials: H
authors.lastname: Huang
authors.affiliation: Chinese Academy of Forestry, Beijing, 100093, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Deng
authors.affiliation: PubBio-Tech Services Corporation, Wuhan 430070, China.
authors.forename: Zhi-Wen
authors.initials: ZW
authors.lastname: Wang
authors.affiliation: PubBio-Tech Services Corporation, Wuhan 430070, China.
authors.forename: Shi-Lin
authors.initials: SL
authors.lastname: Zhu
authors.affiliation: PubBio-Tech Services Corporation, Wuhan 430070, China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Zhao
authors.affiliation: PubBio-Tech Services Corporation, Wuhan 430070, China.
authors.forename: Cao
authors.initials: C
authors.lastname: Deng
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
authors.forename: Shan-Ce
authors.initials: SC
authors.lastname: Niu
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Huang
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.
authors.forename: Meina
authors.initials: M
authors.lastname: Wang
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.
authors.forename: Guo-Hui
authors.initials: GH
authors.lastname: Liu
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.|College of Forestry, South China Agricultural University, Guangzhou, 510640, China.
authors.forename: Hai-Jun
authors.initials: HJ
authors.lastname: Yang
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.
authors.forename: Xin-Ju
authors.initials: XJ
authors.lastname: Xiao
authors.affiliation: Orchid Research Center, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Yu-Yun
authors.initials: YY
authors.lastname: Hsiao
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.|Orchid Research Center, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Wan-Lin
authors.initials: WL
authors.lastname: Wu
authors.affiliation: Dapartment of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.|Orchid Research Center, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: You-Yi
authors.initials: YY
authors.lastname: Chen
authors.affiliation: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki 305-8562, Japan.
authors.forename: Nobutaka
authors.initials: N
authors.lastname: Mitsuda
authors.affiliation: Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan.|Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki 305-8562, Japan.
authors.forename: Masaru
authors.initials: M
authors.lastname: Ohme-Takagi
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
authors.forename: Yi-Bo
authors.initials: YB
authors.lastname: Luo
authors.affiliation: Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics. Ghent University, Ghent, Belgium.|Bioinformatics Institute Ghent, Ghent University, Ghent B-9000, Belgium.|Department of Genetics, Genomics Research Institute, Pretoria, South Africa.
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.|The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China.|College of Forestry, South China Agricultural University, Guangzhou, 510640, China.
authors.forename: Zhong-Jian
authors.initials: ZJ
authors.lastname: Liu
mesh_terms: D001483:Base Sequence; D005075:Biological Evolution; D053898:Biosynthetic Pathways; D031667:Dendrobium / Q000201:enzymology* / Q000235:genetics*; D019143:Evolution, Molecular; D035264:Flowers / Q000235:genetics / Q000254:growth & development*; D017343:Genes, Plant; D018745:Genome, Plant; D016695:Glycosyltransferases / Q000235:genetics* / Q000378:metabolism; D026161:MADS Domain Proteins / Q000235:genetics; D005810:Multigene Family; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D026161:MADS Domain Proteins; D016695:Glycosyltransferases