Integrative transcriptomic and metabolomic analysis of Drynaria roosii reveals genes involved in the biosynthesis of medicinal compounds

The rhizome of Drynaria roosii (Drynariae Rhizoma) holds significant medicinal and economic value. It is traditionally used to promote blood circulation, remove blood stasis, and strengthen the kidneys and bones. However, the distribution and biosynthetic pathways of medicinal compounds in different tissues of D. roosii remain unclear. In this study, non-targeted metabolomics and transcriptomics analyses were conducted on leaves, stems, and tubers of D. roosii, and a high-quality reference transcriptome was obtained using Pacific BioSciences (PacBio) single-molecule real-time (SMRT) sequencing. A total of 1,151 metabolites were identified, including 203 flavonoid-related compounds. Among them, 31 flavonoids-such as quercetin 7-glucoside, tamarixetin, and naringenin 7-rutinoside—were found to be relatively abundant in the tuber. PacBio SMRT sequencing yielded 151,192 consensus reads. A total of 5,581 intron retention (IR) events were identified through alternative splicing analysis, and 56,773 non-redundant transcripts were obtained after transcript redundancy removal. Comparative transcriptome analysis revealed that metabolic pathways such as steroid biosynthesis (ko00100) and phenylpropanoid biosynthesis were enriched in the tuber and leaf. Correlation network analysis identified key genes, including Glycosyltransferase, 4CL, DELLA and others, to be significantly associated with the biosynthesis of naringin 6’'-rhamnoside and naringenin 7-rutinoside. This study provides a foundation for the resource utilization, medicinal compound biosynthesis, and molecular breeding of D. roosii.