Full-length transcriptome profiling of <i>Gentiana straminea</i> Maxim. provides new insights into iridoid biosynthesis pathway

<i>Gentiana straminea</i> Maxim. is a traditional Chinese medicinal plant celebrated for its diverse array of bioactive compounds, particularly iridoid glycosides. These compounds are recognized as the main components that exert therapeutic effects against rheumatism, osteoarthritis, hepatitis, gastritis, and cholecystitis. Consequently, research on <i>G. straminea</i> has attracted significant interest, yet the genetic factors underlying the production and diversification of its secondary metabolites remain poorly understood, especially the pathway of iridoid biosynthesis. In the present study, a full-length transcriptome analysis based on PacBio Sequel II platform and Illumina sequencing was performed to identify genes that were differentially expressed in five <i>G. straminea</i> tissues, and proteins catalyzing iridoid biosynthesis were characterized. After sequence clustering and redundancy removal, a total of 32,776 isoforms were identified in PacBio sequencing, with an average length of 2,589.14 bp, an N50 value of 2,767 bp, and a guanine-cytosine (GC) content of 41.43%. Results of Illumina sequencing unveiled that a total of 31,330 genes were found in common in all the five tissues. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the DEGs were mainly enriched in terms related to biosynthesis of secondary metabolites, metabolic pathways, mitogen-activated protein kinase (MAPK) signaling pathway, <i>etc.</i> A total of 117 isoforms encoding 19 key enzymes related to the iridoid synthesis pathway were identified, including one geranyl diphosphate synthase (GPPS) and two geranylgeranyl diphosphate synthases (GGPPS). A phylogenetic analysis further classified plant G(G)PPSs into three distinct branches. Profiling tissue-specific expression of key genes involved in iridoid synthesis revealed that the Quantitative reverse transcription polymerase chain reaction (RT-qPCR) results demonstrated the consistent trend with the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values in the root, stem, leaf, flower, ovary, non-embryonic callus (NEC), and embryonic callus (EC). Among them, <i>AACT, IDI, ISPH,</i> and <i>GCPE</i> had the highest expression levels in leaves, whereas <i>DXS and GPPS</i> had the highest expression levels in stems. This work provides the first transcriptomic analysis of <i>G. straminea</i>, serving as a foundational resource for elucidating mechanisms of bioactive compound biosynthesis, facilitating molecular studies, and supporting genomic exploration of this medicinal species.