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The Apostasia genome and the evolution of orchids

(2017) NATURE. 549(7672). p.379-383
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth(1-3). Here we report the draft genome sequence of Apostasia shenzhenica(4), a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.
Keywords
MADS-BOX GENES, MULTIPLE SEQUENCE ALIGNMENT, PHYLOGENETIC ANALYSIS, MAXIMUM-LIKELIHOOD, RNA-SEQ, POPULUS-TRICHOCARPA, EUKARYOTIC GENOMES, SUPPLEMENT TREMBL, HIGH-THROUGHPUT, NEW-JERSEY

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Citation

Please use this url to cite or link to this publication:

Chicago
Zhang, Guo-Qiang, Ke-Wei Liu, Zhen Li, Rolf Lohaus, Yu-Yun Hsiao, Shan-Ce Niu, Jie-Yu Wang, et al. 2017. “The Apostasia Genome and the Evolution of Orchids.” Nature 549 (7672): 379–383.
APA
Zhang, G.-Q., Liu, K.-W., Li, Z., Lohaus, R., Hsiao, Y.-Y., Niu, S.-C., Wang, J.-Y., et al. (2017). The Apostasia genome and the evolution of orchids. NATURE, 549(7672), 379–383.
Vancouver
1.
Zhang G-Q, Liu K-W, Li Z, Lohaus R, Hsiao Y-Y, Niu S-C, et al. The Apostasia genome and the evolution of orchids. NATURE. 2017;549(7672):379–83.
MLA
Zhang, Guo-Qiang, Ke-Wei Liu, Zhen Li, et al. “The Apostasia Genome and the Evolution of Orchids.” NATURE 549.7672 (2017): 379–383. Print.
@article{8533332,
  abstract     = {Constituting approximately 10\% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth(1-3). Here we report the draft genome sequence of Apostasia shenzhenica(4), a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.},
  author       = {Zhang, Guo-Qiang and Liu, Ke-Wei and Li, Zhen and Lohaus, Rolf and Hsiao, Yu-Yun and Niu, Shan-Ce and Wang, Jie-Yu and Lin, Yao-Cheng and Xu, Qing and Chen, Li-Jun and Yoshida, Kouki and Fujiwara, Sumire and Wang, Zhi-Wen and Zhang, Yong-Qiang and Mitsuda, Nobutaka and Wang, Meina and Liu, Guo-Hui and Pecoraro, Lorenzo and Huang, Hui-Xia and Xiao, Xin-Ju and Lin, Min and Wu, Xin-Yi and Wu, Wan-Lin and Chen, You-Yi and Chang, Song-Bin and Sakamoto, Shingo and Ohme-Takagi, Masaru and Yagi, Masafumi and Zeng, Si-Jin and Shen, Ching-Yu and Yeh, Chuan-Ming and Luo, Yi-Bo and Tsai, Wen-Chieh and Van de Peer, Yves and Liu, Zhong-Jian},
  issn         = {0028-0836},
  journal      = {NATURE},
  keyword      = {MADS-BOX GENES,MULTIPLE SEQUENCE ALIGNMENT,PHYLOGENETIC ANALYSIS,MAXIMUM-LIKELIHOOD,RNA-SEQ,POPULUS-TRICHOCARPA,EUKARYOTIC GENOMES,SUPPLEMENT TREMBL,HIGH-THROUGHPUT,NEW-JERSEY},
  language     = {eng},
  number       = {7672},
  pages        = {379--383},
  title        = {The Apostasia genome and the evolution of orchids},
  url          = {http://dx.doi.org/10.1038/nature23897},
  volume       = {549},
  year         = {2017},
}

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