The genome sequence of the orchid Phalaenopsis equestris

Authors：Cai Jing; Liu Xin; Vanneste Kevin; Proost Sebastian; Tsai Wen Chieh; Liu Ke Wei; Chen Li Jun; He Ying; Xu Qing; Bian Chao; Zheng Zhijun; Sun Fengming; Liu Weiqing; Hsiao Yu Yun; Pan Zhao Jun; Hsu Chia Chi; Yang Ya Ping; Hsu Yi Chin; Chuang Yu Chen; Dievart Anne; Dufayard Jean Francois; Xu Xun; Wang Jun Yi; Wang Jun; Xiao Xin Ju; Zhao Xue Min; Du Rong; Zhang Guo Qiang; Wang Meina; Su Yong Yu; Xie Gao Chang; Liu Guo Hui; Li Li Qiang; Huang Lai Qiang^*; Luo Yi Bo

Source：Nature Genetics, 2015, 47(1): 65.

DOI：10.1038/ng.3149

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.

• Institution
  华南农业大学; 清华大学; 深圳华大基因研究院; bpotest