Explore the vast range of titles available.

Patchouli ( Pogostemon cablin ) is an aromatic plant, and its oil has diverse applications in medicine, food, and cosmetics. Patchouli alcohol is the principal bioactive constituent of its volatile oil. In China, patchouli is typically categorized into two types: patchoulol-type (PA-type) and pogostone-type (PO-type). The study evaluated physiological and biochemical indicators, phytohormone metabolites and conducted transcriptome and proteome analyses on both two chemotypes. The PA-type exhibited higher levels of chlorophyll a, b, and carotenoids than the PO-type. In total, 35 phytohormone metabolites representing cytokinin, abscisic acid, gibberellin, jasmonic acid, and their derivatives were identified using UPLC-MS/MS, 10 of which displayed significant differences, mainly belong to cytokinins and jasmonates. Transcriptome analysis identified 4,799 differentially expressed genes (DEGs), while proteome analysis identified 150 differentially expressed proteins (DEPs). Regarding the transcriptome results, the DEGs of the PO-type showed significant downregulation in the pathways of photosynthesis, photosynthesis-antenna protein, porphyrin and chlorophyll metabolism, carotenoid biosynthesis, sesquiterpene and triterpenoid biosynthesis, and starch and sucrose metabolism, but upregulation in the pathway of zeatin synthesis. A combination of transcriptome and proteome analyses revealed that the DEGs and DEPs of lipoxygenase (LOX2), β-glucosidase, and patchouli synthase (PTS) were collectively downregulated, while the DEGs and DEPs of Zeatin O-xylosyltransferase (ZOX1) and α-amylase (AMY) were jointly upregulated in the PO-type compared to the PA-type. Differential levels of phytohormones, variations in photosynthetic efficiency, and differential expression of genes in the sesquiterpene synthesis pathway may account for the morphological and major active component differences between the two chemotypes of patchouli. The findings of this study offer novel perspectives on the underlying mechanisms contributing to the formation of the two patchouli chemotypes.

L. is a large genus widely distributed across the continents of the Old World. Among its members, approximately 14 species found in China are recognized as popular herbal medicines. However, accurate authentication of these medicinal species and their phylogenetic relationships with related taxa remains unresolved. To identify simple sequence repeats (SSRs) and divergence hotspot regions appropriate for future authentication studies, as well as to infer the phylogenetic relationships among species, we employed a plastid genome (plastome) dataset consisting of 25 species (21 newly sequenced and four retrieved from GenBank), encompassing 12 Chinese medicinal species, for comparative and phylogenetic analyses. All plastomes displayed a typical quadripartite structure with sizes ranging from 155,948 bp to 157,128 bp and harbored 114 unique genes (80 protein-coding genes, 30 tRNA genes, and four rRNA genes). IRscope and Mauve analyses indicated minimal structural variation among plastomes. We detected between 79 to 95 SSRs across the plastomes; most were located in the large single-copy (LSC) region and primarily consisted of mono-nucleotide repeat sequences (especially A and T repeats). The genus displayed mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide repeats, but with variations in types and numbers among different species. Additionally, we identified 12 special SSR motifs and seven divergent hotspot regions that may serve as potential molecular markers for future identification efforts. Phylogenetic analyses yielded a robust phylogeny for taxa, which were split into Clades I, II, and III. Notably, medicinal species were mainly found in Clade III. Although the phylogenetic relationships of most species aligned with previous study findings, the phylogenetic positions of , , , and were newly determined. The plastomes of are largely conserved in terms of genome structure, size, gene content, and arrangement. Nevertheless, SSRs analyses revealed significant interspecific polymorphism within . In addition, special SSR motifs and divergent hotspot regions identified from plastomes provided reference for subsequent identification investigations. The plastome-based phylogeny provided preliminary insights into the relationships among the Chinese group of medicinal species and related taxa within . Overall, this study offers a wealth of informative genetic resources pertinent to , thereby enhancing our understanding of its evolution and laying a foundation for species identification, assessment of genetic population diversity, as well as the exploration and conservation of germplasm resources.

DC. comprises approximately 100 species with significant morphological diversity. Yet its plastome has rarely been systematically investigated. Previous studies had divided the genus into three main clades: the clade, the clade, and the clade; however, the phylogenetic positions of these clades remain ambiguous. Furthermore, the monophyly of , , , , , and is unresolved and requires further investigation. The exact phylogenetic position of Cass., which has been subsumed into , also remains unclear. To investigate plastome features in , plastomes from 23 species and two varieties (including 23 newly sequenced samples and two publicly available representatives) were compared. Comparative analyses assessed structural and sequence variation, divergence hotspots, simple sequence repeats (SSRs), and codon usage bias. Additionally, phylogenetic inference was performed using a dataset of 47 complete plastomes and 38 nrDNA sequences to reconstruct the backbone phylogeny and address the aforementioned phylogenetic problems. All plastomes exhibited a typical quadripartite structure with sizes ranging from 150,779 bp to 151,281 bp and contained 113 unique genes (79 protein-coding genes, 30 tRNA genes, and four rRNA genes). IRscope and Mauve analyses revealed minimal structural variation among plastomes. Despite the genes flanking each junction being identical, the junction between LSC, SSC, and IRs regions was classified into four types based on the variations in the distances between genes and their respective junctions. Nine divergent hotspot regions were identified as candidate DNA barcodes for future species identification. Between 79 and 95 SSRs were detected per plastome, predominantly in the large single-copy region and mainly comprising mononucleotide repeats. The genus displayed mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide repeats, with specific types and quantities varying among species. Codon usage bias analysis indicated conservation in preferred codon types, numbers, and RSCU values. Phylogenetic analyses consistently supported the division of into four clades: the clade, clade, clade, and clade. Besides, the monophyly of , , , and was well supported. This study conducts the first large-scale comparative analysis of plastomes to date, systematically revealing the conservation and specificity of plastome features of the genus. Phylogeny based on plastome and nrDNA dataset has provided an enhanced phylogenetic framework, and preliminary clarified the phylogeny of the genus. Moreover, the monophyly of taxa including , , , , , and was well examined. In summary, this study provided substantial informative genetic data pertinent to and offered new insights into the phylogeny of , laying the foundation for subsequent taxonomic, systematic, and identification studies.

HD-ZIP IV transcription factors are a plant-specific subgroup of the homeodomain-leucine zipper (HD-ZIP) family, known to regulate epidermal cell differentiation. While their functions have been studied in many plant species, their roles in (patchouli) remain largely unexplored. We conducted a comprehensive genome-wide identification and analysis of genes in patchouli. Phylogenetic relationships, gene structures, conserved motifs, and promoter cis-elements were examined. Expression patterns under hormone treatments were analyzed using qRT-PCR. Correlation analyses and virus-induced gene silencing (VIGS) were employed to assess gene function in glandular trichome development. A total of 38 genes ( ) were identified and classified into six subfamilies. Gene structure and motif analyses revealed conserved features within subgroups. Promoter analysis indicated widespread involvement in light, hormone, and stress responses. Many genes showed dynamic responses to exogenous hormone treatments (MeJA, IAA, SA). Notably, expression correlated strongly with glandular trichome density, and VIGS experiments confirmed its role in promoting trichome development. Our findings suggest that hormone signaling may regulate expression, indirectly influencing glandular trichome formation in patchouli. This study lays a foundation for further functional characterization of genes in patchouli and advances understanding of the molecular mechanisms underlying trichome development.

Plantaginaceae, consisting of 12 tribes, is a diverse, cosmopolitan family. To date, the inter-tribal relationships of this family have been unresolved, and the plastome structure and composition within Plantaginaceae have seldom been comprehensively investigated. In this study, we compared the plastomes from 41 Plantaginaceae species (including 6 newly sequenced samples and 35 publicly representative species) representing 11 tribes. To clarify the inter-tribal relationships of Plantaginaceae, we inferred phylogenic relationships based on the concatenated and coalescent analyses of 68 plastid protein-coding genes. PhyParts analysis was performed to assess the level of concordance and conflict among gene trees across the species tree. The results indicate that most plastomes of Plantaginaceae are largely conserved in terms of genome structure and gene content. In contrast to most previous studies, a robust phylogeny was recovered using plastome data, providing new insights for better understanding the inter-tribal relationships of Plantaginaceae. Both concatenated and coalescent phylogenies favored the sister relationship between Plantagineae and Digitalideae, as well as between Veroniceae and Hemiphragmeae. Sibthorpieae diverged into a separate branch which was sister to a clade comprising the four tribes mentioned above. Furthermore, the sister relationship between Russelieae and Cheloneae is strongly supported. The results of PhyParts showed gene tree congruence and conflict to varying degrees, but most plastid genes were uninformative for phylogenetic nodes, revealing the defects of previous studies using single or multiple plastid DNA sequences to infer the phylogeny of Plantaginaceae.

(Blanco) Benth. also called patchouli, is a traditional medicinal and aromatic plant that grows mainly in Southeast Asia and China. In China, is divided into two chemical types: the patchouliol-type and the pogostone-type. Patchouliol-type patchouli usually grow taller, with thicker stems and bigger leaves, and produce more aromatic oil. To better understand the genetic differences between the two chemical types that contribute to their differences in morphology and biosynthetic capabilities, we constructed transcriptomes from both chemical types using the Pacific Biosciences (PacBio) Sequel platform and performed differential expression analysis of multiple tissues using Illumina short reads. In this study, using single-molecule real-time (SMRT) long-read sequencing, we obtained 22.07 GB of clean data and 134,647 nonredundant transcripts from two chemical types. Additionally, we identified 126,576 open reading frames (ORFs), 100,638 coding sequences (CDSs), 4,106 long noncoding RNAs (lncRNAs) and 6,829 transcription factors (TFs) from two chemical types of . We adopted PacBio and Illumina sequencing to identify differentially expressed transcripts (DEGs) in three tissues of the two chemical types. More DEGs were observed in comparisons of different tissues collected from the same chemical type relative to comparisons of the same tissue collected from different chemical types. Furthormore, using KEGG enrichment analysis of DEGs, we found that the most enriched biosynthetic pathways of secondary metabolites of the two chemical types were \"terpenoid backbone biosynthesis\", \"phenylpropanoid biosynthesis\", \"plant hormone signal transduction\", \"sesquiterpenoid and triterpenoid biosynthesis\", \"ubiquinone and other terpenoid-quinone biosynthesis\", \"flavonoid biosynthesis\", and \"flavone and flavonol biosynthesis\". However, the main pathways of the patchouliol-type also included \"diterpene biosynthesis\" and \"monoterpene biosynthesis\". Additionally, by comparing the expression levels of the three tissues verified by qRT-PCR, more DEGs in the roots were upregulated in the mevalonate (MVA) pathway in the cytoplasm, but more DEGs in the leaves were upregulated in the methylerythritol phosphate (MEP) pathway in the plastid, both of which are important pathways for terpenoids biosynthesis. These findings promote the study of further genome annotation and transcriptome research in .

Background: Polygoni Multiflori Radix (PMR) is a widely distributed herb that has been used for centuries in the treatment of a range of systemic diseases among practitioners of traditional Chinese medicine. Objectives: The present comparative metabolite analysis study was conducted in an effort to understand the relationship between the geographical origin of PMR samples and their medicinal properties. Materials and Methods: As a metabolomics analysis of 35 PMR samples collected from Guangdong and other provinces in China was conducted via ultra-high performance liquid chromatography-quadrupole-electrostatic field orbitrap high-resolution mass spectrometry. Results: Differential metabolite profiles in these PMR samples were evaluated through multivariate statistical analyses. In total, this approach led to the identification of 778 differential metabolites [value of group contribution (VIP) >1, P < 0.01, and fold-change (FC) >2 or <0.5)] that were primarily associated with glycosaminoglycan degradation, lipoic acid metabolism, flavonoid biosynthesis, tyrosine metabolism, flavone and flavonol biosynthesis, phenylpropanoid biosynthesis, and phenylalanine metabolism. Of these metabolites, catechins accounted for seven significantly altered metabolites (VIP ≥2, P < 0.01, and FC >2 or <0.5) when comparing PMR samples from Guangdong with those from other regions. This suggests that PMR samples contain metabolite profiles characteristic of their provenance. Conclusion: As such, metabolomic profiling may be effective means of differentiating between PMR samples from different geographic regions within China, thus providing a sound theoretical basis for the reliable differentiation among and selection of pharmacologically optimal PMR samples.

The complete plastome of Rhoiptelea chiliantha was sequenced and assembled in this study. The circular plastome of R. chiliantha is 161,702 bp in size, which contains a large single-copy region (LSC, 90,447 bp), a short single-copy region (SSC, 19,081 bp) and two inverted repeat sequences (IRs, 26,087 bp, each). It is totally comprised of 133 genes, including 88 protein-coding genes, eight ribosomal RNA, and 37 transfer RNA. The phylogenetic analysis shows that R. chiliantha is sister to the clade including remaining Juglandaceae species.

The complete plastome of Houttuynia cordata, an important medicinal and edible plant, was identified and sequenced in this study. The circular plastome is 160,217 bp in length and consists of a pair of inverted repeats (IRs 26,854 bp each), which is separated by a large single-copy region (LSC, 88,189 bp) and a small single-copy region (SSC, 18,320 bp). It encodes 132 genes, of which 114 are unique genes (80 protein-coding genes, 30 tRNAs, and 4 rRNAs). The phylogenetic analysis strongly reveals the sister group between H. cordata and the clade including Piper kadsura, Piper cenocladum, Saruma henryi, and Asarum sieboldii.

Saururus chinensis is an important medicinal plant in Southeast Asia. Here, we determined the first complete plastome of S. chinensis using high throughput Illumina sequencing technology. The S. chinensis plastome is 161,494 bp in length and presents a typical quadripartite structure consisting of one large single-copy region (LSC, 88,863 bp), one small single-copy region (SSC, 18,679 bp), and a pair of inverted repeat regions (IRs, 26,976 bp each). The phylogenetic analysis robustly supports that S. chinensis is sister to the group including the Saruma henryi, Asarum sieboldii, Piper kadsura, Piper cenocladum.