Niu Zhitao, Zhu Fei, Fan Yajuan, Li Chao, Zhang Benhou, Zhu Shuying, Hou Zhenyu, Wang Mengting, Yang Jiapeng, Xue Qingyun, Liu Wei, Ding Xiaoyu
College of Life Sciences, Nanjing Normal University, China & Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing 210023, China.
Acta Pharm Sin B. 2021 Jul;11(7):2080-2092. doi: 10.1016/j.apsb.2021.01.019. Epub 2021 Feb 2.
, an important medicinal plant of the genus in Orchidaceae family, has been used as traditional Chinese medicine (TCM) for nearly thousands of years. Here, we report the first chromosome-level reference genome of . , based on PacBio long-reads, Illumina short-reads and Hi-C data. The high-quality assembled genome is 1.23 Gb long, with contig N50 of 1.44 Mb. A total of 93.53% genome sequences were assembled into 19 pseudochromosomes with a super scaffold N50 of 63.07 Mb. Through comparative genomic analysis, we explored the expanded gene families of . , and also their impact on environmental adaptation and biosynthesis of secondary metabolites. We further performed detailed transcriptional analysis of , and identified the candidate genes involved in the biosynthesis of three main active ingredients, including polysaccharides, alkaloids and flavonoids. In addition, the () gene, which inferred from Genome-Wide Association Studies (GWAS) based on the resequencing date from and five related species and their morphologic features, may contribute to the plant production (yield of stems) of . Therefore, the high-quality reference genome reported in this study could benefits functional genomics research and molecular breeding of .
[该植物名称]是兰科[属名]的一种重要药用植物，作为传统中药已使用了近千年。在此，我们报告了[该植物名称]的首个染色体水平参考基因组。该基因组基于PacBio长读长、Illumina短读长和Hi-C数据组装而成。高质量组装的基因组长度为1.23 Gb，重叠群N50为1.44 Mb。总共93.53%的基因组序列被组装成19条假染色体，超级支架N50为63.07 Mb。通过比较基因组分析，我们探究了[该植物名称]中扩增的基因家族，以及它们对环境适应和次生代谢物生物合成的影响。我们进一步对[该植物名称]进行了详细的转录分析，并鉴定了参与三种主要活性成分（包括多糖、生物碱和黄酮类化合物）生物合成的候选基因。此外，基于[该植物名称]及其五个近缘物种的重测序数据和形态特征，通过全基因组关联研究（GWAS）推断出的[基因名称]基因，可能对[该植物名称]的植株产量（茎的产量）有贡献。因此，本研究报道的高质量参考基因组将有助于[该植物名称]的功能基因组学研究和分子育种。
