The genome sequence of the orchid Phalaenopsis equestris

Journal name:
Nature Genetics
Volume:
47,
Pages:
65–72
Year published:
DOI:
doi:10.1038/ng.3149
Received
Accepted
Published online
Corrected online
Corrected online

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.

At a glance

Figures

  1. Evolution of P. equestris.
    Figure 1: Evolution of P. equestris.

    (a) Comparison of the number of gene families in orchid (P. equestris), rice (O. sativa), grapevine (V. vinifera) and A. thaliana. (b) Phylogenetic tree and gene family expansion and contraction. The phylogenetic tree was constructed from a concatenated alignment of 72 single-copy gene families from 11 green plant species. Gene family expansions are indicated in orange, and gene family contractions are indicated in gray; the corresponding propotions among total changes are shown using the same colors in the pie charts. Inferred divergence dates (in millions of years) are denoted at each node in blue. MRCA, most recent common ancestor. Blue portions of the pie charts represent the conserved gene families.

  2. Dating the paleopolyploidy event in P. equestris.
    Figure 2: Dating the paleopolyploidy event in P. equestris.

    (a) Absolute age distribution obtained by phylogenomic dating of P. equestris homeologs. The solid black line represents the kernel density estimate of the dated homeologs, and the vertical dashed black line represents its peak, used as the WGD age estimate. Gray lines represent the density estimates for the 1,000 bootstrap replicates, and the vertical black dotted lines represent the corresponding 90% confidence intervals for the WGD age estimate. The original raw distribution of dated homeologs is also indicated by dots. The mode used as an estimate for the consensus WGD age is found at 75.57 million years ago with lower and upper 90% confidence interval boundaries at 71.50 and 80.73 million years ago, respectively y axis represents percentage of gene pairs. (b) Phylogenetic tree of the angiosperms. A wave of WGD events (indicated by colored bars) appears to be associated with the Cretaceous-Paleogene extinction event ~66 million years ago27. The orchid-specific WGD is indicated by the unfilled bar.

  3. Overview of crassulacean acid metabolism (CAM) pathway evolution.
    Figure 3: Overview of crassulacean acid metabolism (CAM) pathway evolution.

    Overview of the CAM pathway with components for which the respective gene family underwent gene duplication or loss as indicated. A star indicates components whose gene families underwent gene loss or gain. CA, carbonic anhydrase; CC, Calvin cycle; PEP, phosphoenolpyruvic acid; PEPC, phosphoenolpyruvate carboxylase; PPCK, phosphoenolpyruvate carboxykinase; MDH, malate dehydrogenase; ME, malic enzyme; PPDK, pyruvate phosphate dikinase.

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Change history

Corrected online 09 January 2015
In the version of this article initially published, the divergence time estimates in Figure 1b were incorrect, and the genome size estimation for Phalaenopsis equestris was incorrectly stated as 1.6 × 106 instead of the correct 1.6 × 109. Finally, Figure 3 incorrectly showed maleic acid in the vacuole reaction, which should have been malic acid. The errors have been corrected in the HTML and PDF versions of the article.
Corrected online 06 February 2015
In the version of this article initially published, the legend for Figure 1b referred to red arrows indicating the inferred divergence dates. No arrows are depicted in the figure, so this sentence has been removed from the figure legend in the HTML and PDF versions of the article.

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Author information

  1. These authors contributed equally to this work.

    • Jing Cai,
    • Xin Liu,
    • Kevin Vanneste,
    • Sebastian Proost,
    • Wen-Chieh Tsai &
    • Ke-Wei Liu

Affiliations

  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.

    • Jing Cai,
    • Ke-Wei Liu,
    • Li-Jun Chen,
    • Xin-Ju Xiao,
    • Guo-Qiang Zhang,
    • Meina Wang,
    • Gao-Chang Xie,
    • Guo-Hui Liu,
    • Li-Qiang Li,
    • Lai-Qiang Huang &
    • Zhong-Jian Liu
  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.

    • Jing Cai,
    • Ke-Wei Liu,
    • Lai-Qiang Huang &
    • Zhong-Jian Liu
  3. School of Life Science, Tsinghua University, Beijing, China.

    • Jing Cai,
    • Ke-Wei Liu &
    • Lai-Qiang Huang
  4. BGI-Shenzhen, Shenzhen, China.

    • Xin Liu,
    • Chao Bian,
    • Zhijun Zheng,
    • Fengming Sun,
    • Weiqing Liu,
    • Xun Xu,
    • Jun-Yi Wang &
    • Jun Wang
  5. Department of Plant Systems Biology, VIB, Ghent, Belgium.

    • Kevin Vanneste,
    • Sebastian Proost,
    • Ying He &
    • Yves Van de Peer
  6. Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.

    • Kevin Vanneste,
    • Sebastian Proost,
    • Ying He &
    • Yves Van de Peer
  7. Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan.

    • Wen-Chieh Tsai
  8. State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.

    • Qing Xu &
    • Yi-Bo Luo
  9. Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.

    • Yu-Yun Hsiao,
    • Zhao-Jun Pan,
    • Chia-Chi Hsu,
    • Ya-Ping Yang,
    • Yi-Chin Hsu,
    • Yu-Chen Chuang &
    • Hong-Hwa Chen
  10. Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Montpellier, France.

    • Anne Dievart &
    • Jean-Francois Dufayard
  11. State Forestry Administration, Beijing, China.

    • Xue-Min Zhao &
    • Rong Du
  12. College of Forestry, South China Agriculture University, Guangzhou, China.

    • Yong-Yu Su,
    • Lai-Qiang Huang &
    • Zhong-Jian Liu
  13. Orchid Research Center, National Cheng Kung University, Tainan, Taiwan.

    • Hong-Hwa Chen
  14. Department of Genetics, Genomics Research Institute, Pretoria, South Africa.

    • Yves Van de Peer

Contributions

J.C., Z.-J.L., L.-Q.H., J.W., H.-H.C., Y.V.d.P., X.L., S.P., K.V., W.-C.T., Y.-B.L., K.-W.L., X.-M.Z. and R.D. planned and coordinated the project and wrote the manuscript. W.-C.T., Y.-Y.S., Z.-J.P., C.-C.H., Y.-P.Y., Y.-C.H., Y.-C.C., L.-J.C., X.-J.X., G.-Q.Z., M.W., G.-C.X., G.-H.L. and L.-Q.L. collected and grew the plant material. J.C., W.-C.T., K.-W.L., L.-J.C. and Q.X. prepared samples. X.L., C.B., Z.Z., W.L., F.S. and K.-W.L. sequenced and processed the raw data. X.L., C.B., Z.Z., X.X., J.W. and F.S. annotated the genome. C.B., X.L., J.C., Y.H. and S.P. analyzed the gene families. C.B., X.L., S.P., K.V., Y.H. and Z.Z. conducted genome evolution analysis. J.C. conducted CAM analysis. J.C., X.L. and F.-M.S. conducted TE insertion analysis. Z.-J.L. and J.-Y.W. conducted protein kinase analysis. W.-C.T., Y.-Y.H., Z.-J.P., C.-C.H., Y.-P.Y., Y.-C.H., Y.-C.C., A.D. and J.-F.D. conducted the MADS-box gene analysis. X.L., J.C. and K.-W.L. conducted transcriptome sequencing and analysis.

Competing financial interests

The authors declare no competing financial interests.

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Supplementary information

PDF files

  1. Supplementary Text and Figures (2,468 KB)

    Supplementary Figures 1–15, Supplementary Tables 1–13, 17 and 21–27, and Supplementary Note.

Excel files

  1. Supplementary Table 14 (9,768 KB)

    Results of the manual check of genes.

  2. Supplementary Table 15 (21 KB)

    GO enrichment analysis of gene family expansion.

  3. Supplementary Table 16 (10 KB)

    GO enrichment analysis of gene family contraction.

  4. Supplementary Table 18 (2,033 KB)

    Reads per kilobase per million mapped reads (RPKM) of all the genes in the four tissues analyzed.

  5. Supplementary Table 19 (37 KB)

    GO enrichment analysis in four tissues.

  6. Supplementary Table 20 (235 KB)

    Allelic genes from heterozygous regions.

Zip files

  1. Supplementary Data Set (76 KB)

    CAM gene alignments.

Additional data