Zhang Yongxia, Zhang Guo-Qiang, Zhang Diyang, Liu Xue-Die, Xu Xin-Yu, Sun Wei-Hong, Yu Xia, Zhu Xiaoen, Wang Zhi-Wen, Zhao Xiang, Zhong Wen-Ying, Chen Hongfeng, Yin Wei-Lun, Huang Tengbo, Niu Shan-Ce, Liu Zhong-Jian
Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518071, China.
Laboratory for Orchid Conservation and Utilization, Orchid Conservation and Research Center, The National Orchid Conservation Center, Shenzhen, 518114, China.
Hortic Res. 2021 Sep 1;8(1):183. doi: 10.1038/s41438-021-00621-z.
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.
作为被子植物中最大的科之一，兰科植物种类繁多。石斛属是兰科的第二大属。然而，该属物种的高质量基因组组装仍属空白。在此，我们报道了重要观赏及药用兰花物种金钗石斛的染色体水平参考基因组。金钗石斛组装后的基因组大小为1.37Gb，重叠群N50值为1.54Mb。其中95.75%的序列被锚定到19条假染色体上。金钗石斛基因组中共预测到30044个基因。金钗石斛发生了两次全基因组多倍化事件。就第二次事件而言，全基因组复制（WGD）也在其他兰科成员中出现，这些成员在WGD事件发生后主要通过基因丢失而分化；第一次复制则发生在大多数单子叶植物中（tau事件）。我们鉴定出糖转运蛋白（SWEET）基因家族扩张，这可能与金钗石斛丰富的药用化合物和肉质茎有关。在金钗石斛中鉴定出了MADS-box基因，以及与抗性相关的TPS和Hsp90基因家族成员，这可能有助于兰花的适应性进化。我们还研究了金钗石斛中类胡萝卜素、脱落酸和乙烯生物合成之间的相互作用，以阐明黄花兰花短花期的调控机制。金钗石斛参考基因组将为进一步研究药用活性成分和育种提供重要见解，并增进对兰花进化的理解。
