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The genome sequence of the orchid Phalaenopsis equestris

(2015) NATURE GENETICS. 47(1). p.65-72
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Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
MAXIMUM-LIKELIHOOD, DATA SETS, POPULUS-TRICHOCARPA, LTR RETROTRANSPOSONS, RNA-SEQ, MOLECULAR PHYLOGENETICS, CRASSULACEAN ACID METABOLISM, MADS-BOX GENES, EVOLUTION, PLANTS

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Citation

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Chicago
Cai, Jing, Xin Liu, Kevin Vanneste, Sebastian Proost, Wen-Chieh Tsai, Ke-Wei Liu, Li-Jun Chen, et al. 2015. “The Genome Sequence of the Orchid Phalaenopsis Equestris.” Nature Genetics 47 (1): 65–72.
APA
Cai, J., Liu, X., Vanneste, K., Proost, S., Tsai, W.-C., Liu, K.-W., Chen, L.-J., et al. (2015). The genome sequence of the orchid Phalaenopsis equestris. NATURE GENETICS, 47(1), 65–72.
Vancouver
1.
Cai J, Liu X, Vanneste K, Proost S, Tsai W-C, Liu K-W, et al. The genome sequence of the orchid Phalaenopsis equestris. NATURE GENETICS. 2015;47(1):65–72.
MLA
Cai, Jing, Xin Liu, Kevin Vanneste, et al. “The Genome Sequence of the Orchid Phalaenopsis Equestris.” NATURE GENETICS 47.1 (2015): 65–72. Print.
@article{5835763,
  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.},
  author       = {Cai, Jing and Liu, Xin and Vanneste, Kevin and Proost, Sebastian and Tsai, Wen-Chieh and Liu, Ke-Wei and Chen, Li-Jun and He, Ying and Xu, Qing and Bian, Chao and Zheng, Zhijun and Sun, Fengming and Liu, Weiqing and Hsiao, Yu-Yun and Pan, Zhao-Jun and Hsu, Chia-Chi and Yang, Ya-Ping and Hsu, Yi-Chin and Chuang, Yu-Chen and Dievart, Anne and Dufayard, Jean-Fran\c{c}ois and Xu, Xun and Wang, Jun-Yi and Wang, Jun and Xiao, Xin-Ju and Zhao, Xue-Min and Du, Rong and Zhang, Guo-Qiang and Wang, Meina and Su, Yong-Yu and Xie, Gao-Chang and Liu, Guo-Hui and Li, Li-Qiang and Huang, Lai-Qiang and Luo, Yi-Bo and Chen, Hong-Hwa and Van de Peer, Yves and Liu, Zhong-Jian},
  issn         = {1061-4036},
  journal      = {NATURE GENETICS},
  keyword      = {MAXIMUM-LIKELIHOOD,DATA SETS,POPULUS-TRICHOCARPA,LTR RETROTRANSPOSONS,RNA-SEQ,MOLECULAR PHYLOGENETICS,CRASSULACEAN ACID METABOLISM,MADS-BOX GENES,EVOLUTION,PLANTS},
  language     = {eng},
  number       = {1},
  pages        = {65--72},
  title        = {The genome sequence of the orchid Phalaenopsis equestris},
  url          = {http://dx.doi.org/10.1038/ng.3149},
  volume       = {47},
  year         = {2015},
}

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