A high-quality chromosomal-level reference genome of Dendrobium nobile Lindl. provides new insights into the biosynthesis and accumulation of picrotoxane-type sesquiterpenoid alkaloids

Dendrobium nobile L., renowned for its ornamental and medicinal attributes, holds significant economic value attributed to its distinct biochemical constituents. A pivotal element within this plant, picrotoxane-type sesquiterpenoid alkaloids (PSAs), exhibits noteworthy anti-hypertensive, anti-cancer, analgesic, and antipyretic properties. However, research on understanding the genes involved in PSAs biosynthesis in D. nobile is very limited. This study provides a quality-enhanced 1.19-Gb genome of D. nobile, featuring a contig N50 of 10.01 Mb, located on 19 chromosomes and encompassing 31,672 protein-coding genes. A comparative genomic analysis reveals expanded gene families within D. nobile, and the implications of these expanded families on the biosynthesis of secondary metabolites were further considered. By incorporating a multifaceted analysis, including researches on gene expansion, tandem duplication, phylogeny, and gene clusters, incorporating the transcriptomics data based on four different expression profiles in D. nobile, the critical candidate genes involved in PSAs biosynthesis were successfully identified. Further implementation of weighted gene co-expression network analysis allowed the identification of 10 transcription factors as potential regulators during PSAs biosynthesis. This study provides valuable insights and genomics resources to elucidate further the evolution and biosynthesis of specialized PSAs, specifically dendrobine.