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Casparian strip integrity factors (CIFs), which are tyrosine-sulfated small peptides, are crucial genes involved in the formation and regulation of the Casparian strip and play an important role in the regulation of plant stress response. In order to explore the evolution, characteristics, role, and function of CIFs in response to continuous cropping obstacles (CCOs), the bioinformatics and gene expression analysis of CIF genes in Pogostemon cablin was carried out by determining the phylogenetic relationship, chromosome location, gene structure, and RT–qPCR results. Results showed that a total of 12 PatCIF family genes were identified on 12 different chromosomes. Promoter prediction analysis revealed 16 different cis-regulatory elements. A systematic evolutionary study of 33 species indicates CIF family genes originated from Spermatophyta. Collinearity analysis revealed P. cablin shared 19 syntenic genes with Solanum lycopersicum and only 8 with Oryza sativa. Transcriptome analysis indicated that the expression of PatCIF1–4 and PatGSO1b/1c/1f genes decreased under p-hydroxybenzoic acid treatment, and further RT–qPCR validation of four PatCIF genes was consistent with the results. AlphaFold prediction showed a protein interaction region between PatCIF1–4 mature peptide and PatGSO1b/1c/1f via the LRR domain, which provides a key binding surface for mature PatCIFs. This study offers a theoretical basis to investigate the roles of PatCIFs and PatGSO1s in CCOs and their protein interactions in P. cablin.

On acid soils, aluminum (Al3+) is typically toxic to plants, though certain species like Pogostemon cablin (patchouli) show growth stimulation. This study reveals that Al functions as a root development stimulant in patchouli under acidic conditions. Treatment with 1.0 mM AlCl3 for 34 days significantly enhanced root architecture, increasing total root length by 172.12% and root dry weight by 161.75%, without affecting shoot biomass. Structural analysis showed Al accumulation in root tip meristems and lateral root primordia, triggering a 103.77% increase in meristem activity and a 111.9% promotion of cell elongation. Physiological assays showed that Al treatment reduced H2O2 and malondialdehyde (MDA) levels by 49.2% and 67.6%, respectively, while boosting glutathione (GSH) content by 187.5%, thereby mitigating oxidative membrane damage mainly through the non-enzymatic antioxidant system. Moreover, Al deprivation impaired lateral root elongation, highlighting its functional importance. Gene expression profiling further indicated that Al regulated pathways related to cell proliferation, cell wall remodeling, and lateral root development. Taken together, our findings uncover a novel mechanism by which Al, traditionally regarded as toxic, acts as a stimulator of root development in patchouli, providing new insights into the molecular networks underlying plant abiotic stress responses.

The JASMONATE ZIM DOMAIN (JAZ) proteins act as negative regulators in the jasmonic acid (JA) signaling pathways of plants, and these proteins have been reported to play key roles in plant secondary metabolism mediated by JA. In this study, we firstly isolated one JAZ from P. cablin, PatJAZ6, which was characterized and revealed based on multiple alignments and a phylogenic tree analysis. The result of subcellular localization indicated that the PatJAZ6 protein was located in the nucleus of plant protoplasts. The expression level of PatJAZ6 was significantly induced by the methyl jasmonate (MeJA). Furthermore, by means of yeast two-hybrid screening, we identified two transcription factors that interact with the PatJAZ6, the PatMYC2b1 and PatMYC2b2. Virus-induced gene silencing (VIGS) of PatJAZ6 caused a decrease in expression abundance, resulting in a significant increase in the accumulation of patchouli alcohol. Moreover, we overexpressed PatJAZ6 in P. cablin, which down-regulated the patchoulol synthase expression, and then suppressed the biosynthesis of patchouli alcohol. The results demonstrate that PatJAZ6 probably acts as a repressor in the regulation of patchouli alcohol biosynthesis, contributed to a model proposed for the potential JA signaling pathway in P. cablin.

Background Plant hormones often cause changes in secondary metabolites. Patchouli alcohol (PA) is a bioactive compound of the medicinal plant Pogostemon cablin . Similar to other secondary metabolites, its synthesis is also regulated by transcription factors. While the PA biosynthetic pathway has been characterized, its regulatory mechanisms remain incompletely understood. Results Transcriptome analysis revealed that exogenous hormone application significantly altered the transcriptional landscape of Pogostemon cablin , particularly affecting genes involved in terpenoid metabolism. Through weighted gene co-expression network analysis (WGCNA), we identified the R2R3-MYB transcription factor gene PcMYB25 as a key candidate regulator. Transient overexpression analysis showed that overexpression of PcMYB25 significantly upregulated PcPTS expression and select upstream MVA pathway genes, and increased PA content by 85% compared to empty vector controls. In addition, yeast one-hybrid assays confirmed that PcMYB25 binds to the PcPTS promoter, and transcriptional activation assays demonstrated its strong transactivation activity. Conclusions We conclude that exogenous hormone treatment triggers an extensive transcriptional response in patchouli, and integrated co-expression analysis identifies PcMYB25 as a candidate regulatory factor involved in plant hormone signaling and the accumulation of PcPTS-derived PA and sesquiterpenoid compounds. These findings not only provide new insights into the transcriptional regulation of PA biosynthesis, but also lay the foundation for further genetic engineering strategies for PA production.

As a strategic resource for both medicine and essential oil, the healthy development of the Pogostemon cablin industry is crucial for the traditional medicine and fragrance sectors. Bacterial wilt represents one of the most significant threats to patchouli cultivation; however, the molecular mechanisms underlying P. cablin ’s response to bacterial wilt remain unexplored. Here, we conducted transcriptome and metabolome analyses, revealing an increase in the expression of genes associated with lipid pathways and a corresponding rise in the concentration of lipid metabolites in P. cablin following infection by the bacterial wilt pathogen SY1 . Further lipidomics analysis demonstrated a significant upregulation of ceramide levels due to SY1 infection. Additionally, hormone analysis indicated that SY1 significantly induced an increase in abscisic acid (ABA) concentration, accompanied by the upregulation of genes involved in the ABA synthesis pathway and its downstream signaling pathways. Furthermore, we treated P. cablin seedlings with the ceramide synthase inhibitor FB1, which significantly reduced ceramide concentration in P. cablin . FB1 treatment also inhibited the expression of ABA-synthesizing genes, leading to a notable decrease in ABA concentration and downstream pathway genes. These data indicate that ceramides and ABA may participate in P. cablin ’s response to SY1 .

Patchoulene, the characteristic sesquiterpene of patchouli essential oil, is highly valued in the perfume industry for its distinctive woody note and fixative properties. Beyond its olfactory applications, patchoulene has demonstrated promising biological activities, including anti-inflammatory, antimicrobial, and neuroprotective effects. Current production relies mainly on extraction from Pogostemon cablin plants, which requires long growth cycles (≥8 months), exhibits low yields, and imposes significant environmental constraints. To overcome these limitations, this study aimed to enhance the Whole-cell yield of patchoulene synthase (PcPTS) through structure-informed protein engineering. A semi-rational design approach was employed, combining homology modeling, molecular docking, evolutionary analysis, and molecular dynamics simulations to identify functional residues within the enzyme active site. Ala-scanning mutagenesis highlighted Thr532 as essential for catalytic activity, and coevolutionary analysis indicated synergistic effects between Phe456 and Thr532. Site-directed mutagenesis was conducted to generate single (F456M, T532Y) and double (F456M/T532Y, designated M2) mutants. The double mutant M2 showed a 3.62-fold increase in patchoulene production compared to the wild-type enzyme. In silico analyses suggested that the enhanced performance of M2 originates from improved substrate positioning, reduced structural flexibility, and strengthened molecular interactions, collectively contributing to a lower energy barrier for catalysis. This study provides an effective strategy for the rapid optimization of terpenoid synthases and facilitates the development of microbial cell factories for sustainable and high-yield production of plant-derived terpenoids.

Pogostemon cablin, the natural source of patchouli alcohol, is an important herb in the Lamiaceae family. Here, we present the entire chloroplast genome of P. cablin. This genome, with 38.24% GC content, is 152,460 bp in length. The genome presents a typical quadripartite structure with two inverted repeats (each 25,417 bp in length), separated by one small and one large single-copy region (17,652 and 83,974 bp in length, respectively). The chloroplast genome encodes 127 genes, of which 107 genes are single-copy, including 79 protein-coding genes, four rRNA genes, and 24 tRNA genes. The genome structure, GC content, and codon usage of this chloroplast genome are similar to those of other species in the family, except that it encodes less protein-coding genes and tRNA genes. Phylogenetic analysis reveals that P. cablin diverged from the Scutellarioideae clade about 29.45 million years ago (Mya). Furthermore, most of the simple sequence repeats (SSRs) are short polyadenine or polythymine repeats that contribute to high AT content in the chloroplast genome. Complete sequences and annotation of P. cablin chloroplast genome will facilitate phylogenic, population and genetic engineering research investigations involving this particular species.

Pogostemon cablin (patchouli) is an economically important aromatic plant widely used in the fragrance and pharmaceutical industries. This study investigates the effects of Corynespora leaf spot disease (CLSD) on the metabolic profiles and patchouli alcohol content of patchouli leaves. Utilizing gas chromatography-mass spectrometry (GC-MS), real-time PCR (qPCR), and comprehensive non-targeted metabolomic analyses (HS-SPME-GC-MS and LC-MS/MS), we compared diseased (LD-TJ) and healthy (CK) leaves. Results revealed a significant 51% reduction in patchouli alcohol content in CLSD-infected leaves, which was correlated with a 94% decrease in expression of the patchoulol synthase (PTS)-encoding gene (p < 0.01) and a 79% reduction in farnesyl pyrophosphate synthase (FPPS)-encoding gene expression (p < 0.05), both critical for terpenoid biosynthesis. Metabolomic analyses identified extensive disruptions in both volatile and non-volatile compounds, with the majority of differential abundance metabolites (DAMs) being downregulated. Key metabolic pathways, including beta-alanine metabolism and nicotinate/nicotinamide metabolism, were notably affected, indicating broader metabolic instability. Additionally, crucial transcription factors involved in terpenoid biosynthesis were significantly downregulated, indicating a potential mechanism by which C. cassiicola may compromise patchouli quality through modulation of host metabolic processes. These findings underscore the urgent need to develop disease-resistant P. cablin cultivars through genetic and metabolic engineering to enhance the sustainability and productivity of this valuable industrial crop.

Patchoulol, a valuable compound belonging to the sesquiterpenoid family, is the primary component of patchouli oil produced by Pogostemon cablin ( P. cablin ). It has a variety of pharmacological and biological activities and is widely used in the medical and cosmetic industries. However, despite its significance, there is a lack of research on the transcriptional modulation of patchoulol biosynthesis. Salicylic acid (SA), is a vital plant hormone that serves as a critical signal molecule and plays an essential role in plant growth and defense. However, to date, no studies have explored the modulation of patchoulol biosynthesis by SA. In our study, we discovered that the application of SA can enhance the production of patchoulol. Utilizing transcriptome analysis of SA-treated P. cablin , we identified a crucial downstream transcription factor, PatWRKY71. The transcription level of PatWRKY71 was significantly increased with the use of SA. Furthermore, our research has revealed that PatWRKY71 was capable of binding to the promoter of PatPTS , ultimately leading to an increase in its expression. When PatWRKY71 was silenced by a virus, the expression of both PatWRKY71 and PatPTS was reduced, resulting in the down-regulation of patchoulol production. Through our studies, we discovered that heterologous expression of PatWRKY71 leads to an increase in the sensitivity of Arabidopsis to salt and Cd, as well as an outbreak of reactive oxygen species (ROS). Additionally, we uncovered the regulatory role of PatWRKY71 in both patchoulol biosynthesis and plant defense response. This discovery provided a theoretical basis for the improvement of the content of patchoulol and the resistance of P. cablin through genetic engineering.

Pogostemon cablin Benth. ( P. cablin ) is an annual aromatic medicinal plant. In this study, anthers were cultured in vitro during the microspore development stage of P. cablin , inducing somatic embryogenesis. Globular somatic embryos (GSE), heart-shaped somatic embryos, torpedo-shaped somatic embryos, and cotyledonary somatic embryos (CSE) were observed and isolated. Single-cell RNA sequencing was then employed to generate single-cell maps for GSE and CSE. Using reported marker genes, a total of eight cell types were identified. Pseudo-temporal analysis reconstructed the continuous differentiation trajectory of apical meristem cells and epidermal cells. Further investigation identified PcNAC048 as a putative transcription factor that regulates embryonic cell differentiation. Gene expression analysis showed PcNAC048 is expressed in different tissues of P. cablin and responds to abiotic stress. Transgenic studies in Arabidopsis thaliana showed that PcNAC048 can promote lateral root development. Results from yeast one - hybrid and dual luciferase assays showed that PcNAC048 can interact with the promoter of the patchouli alcohol synthase gene ( PcPTS ) and inhibit its activity. Transient overexpression and virus-induced gene silencing (VIGS) analysis further confirmed that PcNAC048 can negatively regulate the biosynthesis of patchouli alcohol. Overall, this study provides theoretical support for germplasm development and regulation of medicinal compounds in P. cablin . In patchouli ( Pogostemon cablin ), anther-derived somatic embryos were profiled by single-cell RNA-seq to define eight cell types, identifying PcNAC048 that drives embryonic cell differentiation, promotes lateral root development in Arabidopsis, and negatively regulates patchouli alcohol biosynthesis.