Tissue-specific transcriptome analysis uncovers phenylpropanoid biosynthetic genes in Althaea officinalis

Abstract

Althaea officinalis is a medicinal plant, rich in mucilage and polyphenols and traditionally used to relieve inflammation and irritation of respiratory, digestive, and urinary tissues. This study presents the first comprehensive transcriptomic analysis of A. officinalis revealing dynamic polyphenol biosynthesis patterns across flower, leaf, and root tissues. Phytochemical analysis showed that flowers have the highest total phenolic content (6.07 mg GAE/g), while leaves are richest in flavonoids (4.38 mg RE/g). Our analysis identified 295,087 unigenes and 16,551 differentially expressed genes (DEGs) including 225 DEGs in the phenylpropanoid pathway. We report the first identification of candidate genes for lignan and isoflavone biosynthesis in this species. The results showed that roots are characterized by a high expression of the lignin-coumarin axis genes such as 4CL1, CCR2, CCoAOMT and CAD1, whereas flowers exhibit activation of the flavonoid branch through CHS1, CHI, and FLS. Additionally, leaves were enriched in B-ring hydroxylation genes including F3’H and F3’5’H. Phylogenetic analysis of 14 AoCHS unigenes confirmed their evolutionary conservation within the Malvaceae family. RT-qPCR analysis of key candidate genes validated the expression patterns observed in the RNA-Seq data, confirming the reliability of the transcriptomic profile. These findings elucidate the molecular basis of bioactive compound biosynthesis, providing a genomic foundation for phytopharmaceutical application of A. officinalis .