Mentha is a commonly used spice worldwide, which possesses medicinal properties and fragrance. These characteristics are conferred, at least partially, by essential oils such as menthol. In this study, a gap-free assembly with a genome size of 414.3 Mb and 31,251 coding genes was obtained for Mentha suaveolens ‘Variegata’. Based on its high heterozygosity (1.5%), two complete haplotypic assemblies were resolved, with genome sizes of 401.9 and 405.7 Mb, respectively. The telomeres and centromeres of each haplotype were almost fully annotated. In addition, we detected a total of 41,135 structural variations. Enrichment analysis demonstrated that genes involved in terpenoid biosynthesis were affected by these structural variations. Analysis of volatile metabolites showed that M. suaveolens mainly produces piperitenone oxide rather than menthol. We identified three genes in the M. suaveolens genome which encode isopiperitenone reductase (ISPR), a key rate-limiting enzyme in menthol biosynthesis. However, the transcription levels of ISPR were low. Given that other terpenoid biosynthesis genes were expressed, M. suaveolens ISPRs may account for the accumulation of piperitenone oxide in this species. The findings of this study may provide a valuable resource for improving the detection rate and accuracy of genetic variants, thereby enhancing our understanding of their impact on gene function and expression. Moreover, our haplotype-resolved gap-free genome assembly offers novel insights into molecular marker-assisted breeding of Mentha.

For steady transgenic expression, lentiviral vector-mediated gene delivery is a commonly used technique. One question that needs to be explored is how external lentiviral vectors and overexpressed genes perturb cellular homeostasis, potentially altering transcriptional networks. In this study, two Human Embryonic Kidney 293T (HEK293T)-derived cell lines were established via lentiviral transduction, one overexpressing green fluorescent protein (GFP) and the other co-overexpressing GFP and ADORA3 following puromycin selection to ensure stable genomic integration. Genes with differentially transcript utilization (gDTUs) and differentially expressed genes (DEGs) across cell lines were identified after short-read and long-read RNA-seq. Only 31 genes were discovered to have changed in expression when GFP was expressed, although hundreds of genes showed variations in transcript use. In contrast, even when co-overexpression of GFP and ADORA3 alters the expression of more than 1000 genes, there are still less than 1000 gDTUs. Moreover, DEGs linked to ADORA3 overexpression play a major role in RNA splicing, whereas gDTUs are highly linked to a number of malignancies and the molecular mechanisms that underlie them. For the analysis of gene expression data from stable cell lines derived from HEK293T, our findings provide important insights into changes in gene expression and alternative splicing.

Background: Ligusticum chuanxiong Hort. is a well-known traditional Chinese medicinal herb whose clinical application and international trade had been constrained by cadmium (Cd) contamination. However, the molecular mechanisms underlying its response to cadmium stress remained poorly understood. The ATP-binding cassette (ABC) transporter family plays crucial roles in various plant processes, including growth and development, hormone transduction, and stress responses. This study aimed to analyze the ABC transporter genes in L. chuanxiong to better understand their roles during cadmium stress responses. Methods: Genome-wide identification of ABC genes in L. chuanxiong was performed, and transcriptome sequencing of rhizomes under cadmium stress was conducted. Differentially expressed LcABC genes were screened using bioinformatic analysis. Results: A total of 368 LcABC genes were identified. Transcriptome analysis revealed 37 upregulated LcABC genes, which were classified into six subfamilies. Cis-element analysis indicated that their promoters contain hormone-, growth-, and stress-responsive elements. Notably, LcABCG8, LcABCG48, and LcABCG108 contain stress-responsive elements and show close evolutionary relationships with heavy metal-responsive genes such as AtABCC1/2/3 and AtABCG36/40, suggesting that they could be key candidates. qRT-PCR validation of nine LcABC genes confirmed their differential sensitivity to cadmium stress. Conclusions: This study conducted a comprehensive identification of the ABC gene family in L. chuanxiong. By integrating transcriptomic data with systematic bioinformatic analyses, we identified several LcABC transporters that may play important roles in cadmium stress responses. The results provide insights into the molecular mechanisms of ABC transporters in cadmium stress responses in L. chuanxiong and offer strategies for reducing cadmium accumulation.

MicroRNAs are a group of endogenous small non-coding RNAs, they can guide silencing complex to degrade mRNA or hinder its translation by pairing with the target gene mRNA base. In this study, applying high stringent genome-wide computational-based approaches, a total of 31 putative microRNAs were predicted in Stephania japonica. After strict secondary structure screening, seven microRNAs with high reliability were identified and classified into three microRNA families. Using Targetfinder tool, a total of 47 potential target transcription factors of microRNAs were identified, including bHLH, SBP, TCP, ERF transcription factors. The co-expression network of transcription factors and three important cepharanthine-biosynthetic genes shown that microRNAs might be involved in regulating the biosynthesis of cepharanthine and its precursors by regulating potential target transcription factors. Additionally, correlation analysis of microRNAs and transcription factors indicated that the tissue expression patterns of Sja-miR8528, Sja-miR156a and Sja-miR156c showed positive correlation with six transcription factors, while Sja-miR535 showed a negative correlation with five transcription factors. This is the first study explored putative microRNA and analyzed their predictive target transcription factors in S. japonica, providing useful information for future microRNA research in herbal plants.

Renal fibrosis (RF) represents the pathognomonic end-stage phenotype of progressive nephropathies, pathologically characterized by excessive deposition of fibrillar extracellular matrix (ECM) and irreversible obliteration of parenchymal architecture. G protein-coupled receptors (GPCRs)—members of the heptahelical transmembrane receptor superfamily—function as master regulators orchestrating both physiological renal homeostasis and maladaptive fibrotic reprogramming in response to injury. Despite robust clinical evidence validating the therapeutic tractability of GPCR-targeted interventions for chronic kidney disease (CKD), no approved agents specifically antagonize the core pathogenic drivers of RF. Consequently, this review systematically delineates GPCRs exhibiting mechanistic primacy in RF pathobiology and translational promise, with focused interrogation of endothelin receptors, angiotensin receptors, chemokine receptors, and adenosine receptors. Beyond canonical modulation of inflammatory leukocyte infiltration and pro-fibrotic phenotypic transitions, emerging paradigms highlight GPCR governance over metabolomic reprogramming and mechanotransductive signaling during fibrogenesis. Notwithstanding these mechanistic advances, clinical translation of GPCR-directed anti-fibrotic therapeutics remains nascent, constrained by target pleiotropy, biodistribution barriers, and species-divergent pathophysiology. Collectively, GPCRs constitute high-value molecular targets for intercepting the progression of RF at its mechanistic nexus.

Introduction: Aconitum pendulum is a well-known Tibetan medicine that possesses abundant diterpenoid alkaloids (DAs) with high medicinal value. However, due to the complicated structures of DAs and the associated challenges in vitro synthesis presents, plants like Aconitum pendulum remain the primary source for DAs.Methods: Given the underutilization of the A. pendulum, a thorough metabolomic and transcriptomic analysis was conducted on its flowers, leaves, and stems to elucidate the regulatory network underlying DA biosynthesis.Results: Metabolomic profiling (utilizing UPLC-QQQ-MS/MS) identified 198 alkaloids, of which 61 were DAs and the relative abundance of DAs was different among different tissues. Without a reference genome, we performed de novo assembly of the transcriptome of A. pendulum. We generated 181,422 unigenes, among which 411 candidate enzyme genes related to the DA synthesis pathway were identified, including 34 differentially expressed genes (DEGs). Through joint analysis of transcriptome and metabolome data, we found a correlation between the detected metabolite levels in various tissues and the expression of related genes. Specifically, it was found that ApCYP1, ApCYP72, and ApCYP256 may be related to turupellin accumulation, while ApBAHD9, ApBAHD10, ApBAHD12 positively associated with the accumulation of aconitine. Furthermore, our study also revealed that genes involved in the diterpene skeleton synthesis pathway tend to be highly expressed in flowers, whereas genes related to DA skeleton synthesis and their subsequent modifications are more likely to be highly expressed in leaf and stem tissues. Functional analysis of gene families identified 77 BAHD acyltransferases, 12 O-methyltransferases, and 270 CYP450 enzyme genes potentially involved in the biosynthesis of DAs. The co-expression network between metabolites and related genes revealed 116 significant correlations involving 30 DAs and 58 enzyme genes.Discussion: This study provides valuable resources for in-depth research on the secondary metabolism of A. pendulum, not only deepening our understanding of the regulatory mechanisms of DA biosynthesis but also providing valuable genetic resources for subsequent genetic improvement and metabolic engineering strategies.