Deciphering the Biosynthetic Pathways and Regulatory Networks of the Active Components of Cibotium barometz by Transcriptomic Analysis

<i>Cibotium barometz</i> (L.) J. Sm., a medicinally significant fern in traditional Chinese medicine, is little explored at the genomic level regarding its bioactive compounds. Using an integrated approach combining Illumina and PacBio sequencing technologies, we profiled its root, rachis, and pinna transcriptomes, identifying 12,718, 21,341, and 11,441 unigenes, respectively. Our analysis systematically characterized the transcriptional features of transcription factors (TFs), simple sequence repeats (SSRs), long non-coding RNAs (lncRNAs), and differentially expressed genes (DEGs). Enrichment analyses highlighted the roles of highly expressed unigenes in secondary metabolism. Seventeen key enzymes involved in polysaccharide biosynthesis showed tissue-specific expression patterns. Notably, total polysaccharide content correlated positively with UDP-arabinose 4-epimerase (<i>UXE</i>) expression but negatively with phosphoglucomutase (<i>PGM</i>) and 3,5-epimerase/4-reductase (<i>UER1</i>). Flavonoid accumulation inversely correlated with chalcone synthase (<i>CHS</i>) expression. Two lignin pathways (H-lignin and G-lignin) were characterized, with phenylalanine ammonia-lyase (<i>PAL</i>), cinnamate-4-hydroxylase (<i>C4H</i>), and cinnamyl alcohol dehydrogenase (<i>CAD</i>) as key genes. The absence of ferulate-5-hydroxylase (<i>F5H</i>) explains the undetected S-lignin pathway. Regulatory network analysis revealed positive correlations between <i>PAL</i> expression and <i>NAC72</i>/<i>NAC78</i>/<i>WRKY35</i> and <i>C4H</i> expression and <i>WRKY65</i>/<i>WRKY69</i>/<i>WRKY71</i>, while a negative correlation was revealed between flavonoid 3',5'-hydroxylase (<i>F3'5'H</i>) and <i>MYB3R4</i>. This study provides comprehensive transcriptomic insights into <i>C. barometz</i> bioactive compound biosynthesis, serving as a foundation for mechanistic research.