Chromosome-scale genome assembly, carbohydrate metabolism transcriptome atlas, and candidate genes for polysaccharide accumulation in Asparagus cochinchinensis

Asparagus cochinchinensis is a valued medicinal plant, whose bioactive polysaccharides are important secondary metabolites. However, the evolutionary origins and spatiotemporal regulation of their biosynthesis remain unclear, hindered by the lack of a reference genome. Here, by combining PacBio HiFi, Illumina, and Hi-C sequencing technologies, we generated the first publicly available chromosome-level genome assembly of A. cochinchinensis (1.52 Gb; 10 pseudochromosomes). We annotated 48, 453 protein-coding genes and dated the divergence of Asparagus from Orchidaceae to ~95 million years ago. Comparative genomics revealed lineage-specific whole-genome duplication events and gene family expansions linked to metabolic adaptation. To identify candidate genes associated with polysaccharide accumulation, we generated transcriptomes from root tuber, fibrous root, leaf, and spear tissues. Co-expression network and pathway analyses identified 16 key genes significantly associated with polysaccharide accumulation, particularly in underground storage organs. Our analysis reconstructs the sucrose-to-polysaccharide biosynthetic pathway and highlights differential gene expression between tuber and fibrous root tissues, revealing the spatial compartmentalization of this metabolic process. This high-quality genome provides a foundational resource for elucidating the evolution and tissue-specific regulation of secondary metabolite biosynthesis in Asparagus , with implications for molecular breeding aimed at enhancing medicinal compound yield.