The genome sequence of the orchid Phalaenopsis equestris

Jing Cai¹, Xin Liu², Kevin Vanneste³, Sebastian Proost³, Wen-Chieh Tsai⁴, Ke-Wei Liu¹, Li-Jun Chen⁵, Ying He³, Qing Xu⁶, Chao Bian², Zhijun Zheng², Fengming Sun², Weiqing Liu², Yu-Yun Hsiao⁷, Zhao-Jun Pan⁷, Chia-Chi Hsu⁷, Ya-Ping Yang⁷, Yi-Chin Hsu⁷, Yu-Chen Chuang⁷, Anne Dievart⁸, Jean-Francois Dufayard⁸, Xun Xu², Jun-Yi Wang², Jun Wang², Xin-Ju Xiao⁵, Xue-Min Zhao⁹, Rong Du⁹, Guo-Qiang Zhang⁵, Meina Wang⁵, Yong-Yu Su¹⁰, Gao-Chang Xie⁵, Guo-Hui Liu⁵, Li-Qiang Li⁵, Lai-Qiang Huang¹¹, Yi-Bo Luo⁶, Hong-Hwa Chen¹², Yves Van de Peer¹³, Zhong-Jian Liu¹⁴

Affiliations

¹ 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.
² BGI-Shenzhen, Shenzhen, China.
³ 1] Department of Plant Systems Biology, VIB, Ghent, Belgium. [2] Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
⁴ Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan.
⁵ Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China.
⁶ State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
⁷ Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
⁸ Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Montpellier, France.
⁹ State Forestry Administration, Beijing, China.
¹⁰ College of Forestry, South China Agriculture University, Guangzhou, China.
¹¹ 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.
¹² 1] Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan. [2] Orchid Research Center, National Cheng Kung University, Tainan, Taiwan.
¹³ 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.
¹⁴ 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.

PMID: 25420146
DOI: 10.1038/ng.3149

Comparative Study

The genome sequence of the orchid Phalaenopsis equestris

Jing Cai et al. Nat Genet. 2015 Jan.

. 2015 Jan;47(1):65-72.

doi: 10.1038/ng.3149. Epub 2014 Nov 24.

Authors

Affiliations

¹ 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.
² BGI-Shenzhen, Shenzhen, China.
³ 1] Department of Plant Systems Biology, VIB, Ghent, Belgium. [2] Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
⁴ Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan.
⁵ Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China.
⁶ State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
⁷ Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
⁸ Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Montpellier, France.
⁹ State Forestry Administration, Beijing, China.
¹⁰ College of Forestry, South China Agriculture University, Guangzhou, China.
¹¹ 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.
¹² 1] Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan. [2] Orchid Research Center, National Cheng Kung University, Tainan, Taiwan.
¹³ 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.
¹⁴ 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.

PMID: 25420146
DOI: 10.1038/ng.3149

Erratum in

Corrigendum: The genome sequence of the orchid Phalaenopsis equestris.
Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, Chen LJ, He Y, Xu Q, Bian C, Zheng Z, Sun F, Liu W, Hsiao YY, Pan ZJ, Hsu CC, Yang YP, Hsu YC, Chuang YC, Dievart A, Dufayard JF, Xu X, Wang JY, Wang J, Xiao XJ, Zhao XM, Du R, Zhang GQ, Wang M, Su YY, Xie GC, Liu GH, Li LQ, Huang LQ, Luo YB, Chen HH, Van de Peer Y, Liu ZJ. Cai J, et al. Nat Genet. 2015 Mar;47(3):304. doi: 10.1038/ng0315-304a. Nat Genet. 2015. PMID: 25711871 No abstract available.

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.

PubMed Disclaimer

Comment in

A genome to unveil the mysteries of orchids.
Albert VA, Carretero-Paulet L. Albert VA, et al. Nat Genet. 2015 Jan;47(1):3-4. doi: 10.1038/ng.3179. Nat Genet. 2015. PMID: 25547596

Publication types

Actions
Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions

Substances

Actions
Actions
Actions
Actions

Associated data

BioProject/PRJNA192198

LinkOut - more resources

Full Text Sources
- Nature Publishing Group
Other Literature Sources
- The Lens - Patent Citations Database
- scite Smart Citations

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

The genome sequence of the orchid Phalaenopsis equestris

Affiliations

The genome sequence of the orchid Phalaenopsis equestris

Authors

Affiliations

Erratum in

Abstract

Comment in

Publication types

MeSH terms

Substances

Associated data

LinkOut - more resources

Full Text Sources

Other Literature Sources