The Apostasia genome and the evolution of orchids

Guo Qiang Zhang, Ke Wei Liu, Zhen Li, Rolf Lohaus, Yu Yun Hsiao, Shan Ce Niu, Jie Yu Wang, Yao Cheng Lin, Qing Xu, Li Jun Chen, Kouki Yoshida, Sumire Fujiwara, Zhi Wen Wang, Yong Qiang Zhang, Nobutaka Mitsuda, Meina Wang, Guo Hui Liu, Lorenzo Pecoraro, Hui Xia Huang, Xin Ju XiaoMin Lin, Xin Yi Wu, Wan Lin Wu, You Yi Chen, Song Bin Chang, Shingo Sakamoto, Masaru Ohme-Takagi, Masafumi Yagi, Si Jin Zeng, Ching Yu Shen, Chuan Ming Yeh, Yi Bo Luo, Wen Chieh Tsai, Yves Van De Peer, Zhong Jian Liu

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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. Here we report the draft genome sequence of Apostasia shenzhenica, 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.

Original languageEnglish
Pages (from-to)379-383
Number of pages5
JournalNature
Volume549
Issue number7672
DOIs
Publication statusPublished - 2017 Sep 21

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Zhang, G. Q., Liu, K. W., Li, Z., Lohaus, R., Hsiao, Y. Y., Niu, S. C., Wang, J. Y., Lin, Y. C., Xu, Q., Chen, L. J., Yoshida, K., Fujiwara, S., Wang, Z. W., Zhang, Y. Q., Mitsuda, N., Wang, M., Liu, G. H., Pecoraro, L., Huang, H. X., ... Liu, Z. J. (2017). The Apostasia genome and the evolution of orchids. Nature, 549(7672), 379-383. https://doi.org/10.1038/nature23897