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Article|01 Sep 2021|OPEN
Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution
Yongxia Zhang1, Guo-Qiang Zhang2,3, Diyang Zhang4, Xue-Die Liu4,5, Xin-Yu Xu4, Wei-Hong Sun4,5, Xia Yu4, Xiaoen Zhu1, Zhi-Wen Wang6, Xiang Zhao6, Wen-Ying Zhong6, Hongfeng Chen7, Wei-Lun Yin4,8, Tengbo Huang1,, Shan-Ce Niu9 & Zhong-Jian Liu4,
1Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518071, China
2Laboratory for Orchid Conservation and Utilization, Orchid Conservation and Research Center, The National Orchid Conservation Center, Shenzhen 518114, China
3School of Food Science and Technology, Foshan University, Foshan 528225, China
4Key Laboratory of National Forestry and Grassland Zhang et al. Horticulture Research (2021) 8:183 Page 12 of 14 Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
5College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
6PubBio-Tech, Wuhan 430070, China
7Key Laboratory of Plant Resources Conservation Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
8College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
9College of Horticulture, Hebei Agricultural University, Baoding 071000, China

Horticulture Research 8,
Article number: 183 (2021)
doi: 10.1038/hortres.2021.183
Views: 56

Received: 06 Jan 2021
Revised: 23 Apr 2021
Accepted: 01 Jun 2021
Published online: 01 Sep 2021

Abstract

As one of the largest families of angiosperms, the Orchidaceae family is diverse. Dendrobium represents the second largest genus of the Orchidaceae. However, an assembled high-quality genome of species in this genus is lacking. Here, we report a chromosome-scale reference genome of Dendrobium chrysotoxum, an important ornamental and medicinal orchid species. The assembled genome size of D. chrysotoxum was 1.37 Gb, with a contig N50 value of 1.54 Mb. Of the sequences, 95.75% were anchored to 19 pseudochromosomes. There were 30,044 genes predicted in the D. chrysotoxum genome. Two whole-genome polyploidization events occurred in D. chrysotoxum. In terms of the second event, whole-genome duplication (WGD) was also found to have occurred in other Orchidaceae members, which diverged mainly via gene loss immediately after the WGD event occurred; the first duplication was found to have occurred in most monocots (tau event). We identified sugar transporter (SWEET) gene family expansion, which might be related to the abundant medicinal compounds and fleshy stems of D. chrysotoxum. MADS-box genes were identified in D. chrysotoxum, as well as members of TPS and Hsp90 gene families, which are associated with resistance, which may contribute to the adaptive evolution of orchids. We also investigated the interplay among carotenoid, ABA, and ethylene biosynthesis in D. chrysotoxum to elucidate the regulatory mechanisms of the short flowering period of orchids with yellow flowers. The reference D. chrysotoxum genome will provide important insights for further research on medicinal active ingredients and breeding and enhances the understanding of orchid evolution.