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The Apostasia genome and the evolution of orchids

Guo-Qiang Zhang, Ke-Wei Liu, Zhen Li UGent, Rolf Lohaus UGent, Yu-Yun Hsiao, Shan-Ce Niu, Jie-Yu Wang, Yao-Cheng Lin, Qing Xu, Li-Jun Chen, et al. (2017) NATURE. 549(7672). p.379-383
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
MADS-BOX GENES, MULTIPLE SEQUENCE ALIGNMENT, PHYLOGENETIC ANALYSIS, MAXIMUM-LIKELIHOOD, RNA-SEQ, POPULUS-TRICHOCARPA, EUKARYOTIC GENOMES, SUPPLEMENT TREMBL, HIGH-THROUGHPUT, NEW-JERSEY
journal title
NATURE
Nature
volume
549
issue
7672
pages
379 - 383
Web of Science type
Article
Web of Science id
000411381300034
ISSN
0028-0836
1476-4687
DOI
10.1038/nature23897
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
additional info
the first four authors contributed equally to this work
copyright statement
Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
id
8533332
handle
http://hdl.handle.net/1854/LU-8533332
date created
2017-10-05 14:12:26
date last changed
2017-11-07 08:50:24
@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},
}

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.