The chromosome-level reference genome assembly for and its utility of functional genomics research and molecular breeding study.

, 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 .