Zhang Guo-Qiang, Liu Ke-Wei, Li Zhen, Lohaus Rolf, Hsiao Yu-Yun, Niu Shan-Ce, Wang Jie-Yu, Lin Yao-Cheng, Xu Qing, Chen Li-Jun, Yoshida Kouki, Fujiwara Sumire, Wang Zhi-Wen, Zhang Yong-Qiang, Mitsuda Nobutaka, Wang Meina, Liu Guo-Hui, Pecoraro Lorenzo, Huang Hui-Xia, Xiao Xin-Ju, Lin Min, Wu Xin-Yi, Wu Wan-Lin, Chen You-Yi, Chang Song-Bin, Sakamoto Shingo, Ohme-Takagi Masaru, Yagi Masafumi, Zeng Si-Jin, Shen Ching-Yu, Yeh Chuan-Ming, Luo Yi-Bo, Tsai Wen-Chieh, Van de Peer Yves, Liu Zhong-Jian
Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.
Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
Nature. 2017 Sep 21;549(7672):379-383. doi: 10.1038/nature23897. Epub 2017 Sep 13.
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.
兰花（兰科）约占开花植物物种的10%，展现出独特的花形态，生活方式具有非凡的多样性，并且已成功占据了地球上几乎每一个栖息地。在此，我们报告了深圳拟兰的基因组草图序列，深圳拟兰是构成兰科其他类群姐妹谱系的两个属之一的代表，为推断所有现存兰花最近共同祖先的基因组内容和结构以及增进我们对其起源和演化的理解提供了参考。此外，我们还展示了香荚兰亚科、杓兰亚科和红门兰亚科代表的转录组数据，以及两个附生兰亚科物种的全新第三代基因组数据，涵盖了所有五个兰花亚科。深圳拟兰显示出全基因组复制的明确证据，这一现象为所有兰花所共有，且发生在它们分化前不久。通过对深圳拟兰与其他兰花及被子植物的比较，还得以重建兰花祖先基因工具包。我们识别出了新的基因家族、基因家族的扩张和收缩，以及在兰花演化过程中控制多种发育过程的MADS盒基因类别的变化。这项研究为兰花关键创新背后的遗传机制带来了新的认识，这些创新包括唇瓣和蕊柱、花粉块以及无胚乳种子的发育，还有附生习性的演化；揭示了兰科各亚科之间的关系；并有助于厘清兰花在被子植物中的演化历史。
