Callerya speciosa (Champ. ex Benth.) Schot is a traditional Chinese medicine characterized by tuberous roots as the main organ of isoflavonoid accumulation. Root thickening and isoflavonoid accumulation are two major factors for yield and quality of C. speciosa. However, the underlying mechanisms of root thickening and isoflavonoid biosynthesis have not yet been elucidated. Here, integrated morphological, hormonal and transcriptomic analyses of C. speciosa tuberous roots at four different ages (6, 12, 18, 30 months after germination) were performed. The growth cycle of C. speciosa could be divided into three stages: initiation, rapid-thickening and stable-thickening stage, which cued by the activity of vascular cambia. Endogenous changes in phytohormones were associated with developmental changes during root thickening. Jasmonic acid might be linked to the initial development of tuberous roots. Abscisic acid seemed to be essential for tuber maturation, whereas IAA, cis-zeatin and gibberellin 3 were considered essential for rapid thickening of tuberous roots. A total of 4337 differentially expressed genes (DEGs) were identified during root thickening, including 15 DEGs participated in isoflavonoid biosynthesis, and 153 DEGs involved in starch/sucrose metabolism, hormonal signaling, transcriptional regulation and cell wall metabolism. A hypothetical model of genetic regulation associated with root thickening and isoflavonoid biosynthesis in C. speciosa is proposed, which will help in understanding the underlying mechanisms of tuberous root formation and isoflavonoid biosynthesis.

Gynostemma pentaphyllum an important medicinal herb, can absorb high amounts of cadmium (Cd) which can lead to excessive Cd contamination during the production of medicines and tea. Hence, it is crucial to investigate the response mechanism of G. pentaphyllum under Cd stress to develop varieties with low Cd accumulation and high tolerance. Physiological response analysis, transcriptomics and metabolomics were performed on G. pentaphyllum seedlings exposed to Cd stress. Herein, G. pentaphyllum seedlings could significantly enhance antioxidant enzyme activities (POD, CAT and APX), proline and polysaccharide content subject to Cd stress. Transcriptomics analysis identified the secondary metabolites, carbohydrate metabolism, amino acid metabolism, lipid metabolism, and signal transduction pathways associated with Cd stress, which mainly involved the XTH, EXP and GST genes. Metabolomics analysis identified 126 differentially expressed metabolites, including citric acid, flavonoid and amino acids metabolites, which were accumulated under Cd stress. Multi-omics integrative analysis unraveled that the phenylpropanoid biosynthesis, starch, and sucrose metabolism, alpha-linolenic acid metabolism, and ABC transporter were significantly enriched at the gene and metabolic levels in response to Cd stress in G. pentaphyllum. In conclusion, the genetic regulatory network sheds light on Cd response mechanisms in G. pentaphyllum.

The tubers of Curcuma kwangsiensis are regarded as an important medicinal material in China. In C. kwangsiensis cultivation, tuber expansion is key to yield and quality, but the regulatory mechanisms are not well understood. In this study, metabolomic and transcriptomic analyses were conducted to elucidate the mechanism underlying tuber expansion development. The results showed that auxin (IAA), jasmonic acid (JA), gibberellin (GA₃₎, ethylene (ETH), and brassinolide (BR) levels increased during tuber expansion development. Metabolomic analysis showed that 197 differentially accumulated metabolites (DAMs) accumulated during tuber expansion development and these also play important roles in the accumulation of carbohydrates and secondary metabolites. 6962 differentially expressed genes (DEGs) were enriched in plant hormone signal transduction, starch and sucrose metabolism, linoleic acid metabolism, MAPK signaling pathway as well as sesquiterpenoid and triterpenoid biosynthesis. Comprehensive analysis revealed that DEGs and DAMs of plant hormone signal transduction, ABC transporters and biosynthesis of phenylpropanoids and terpenoids are critical pathways in regulating tuber expansion. In addition, some transcription factors (ARF, C2H2, C3H, NAC, bHLH, GRAS and WRKY) as well as hub genes (HDS, HMGR, ARF7, PP2CA, PAL and CCOMT) are also involved in this process. This study lays a theoretical basis for the molecular mechanism of tuber expansion in C. kwangsiensis.

Gynostemma pentaphyllum , a perennial medicinal herb, is widely distributed and exhibits remarkable adaptability to various environments. WRKY transcription factors play critical roles in regulating plant growth and development, as well as abiotic stress responses. However, the WRKY genes in G. pentaphyllum and their expression patterns under different tissues and Cd stress have not been thoroughly investigated, hindering our understanding of their role. In this study, 64 WRKY transcription factors identified in the G. pentaphyllum genome ( GpWRKY ) were phylogenetically grouped into three major groups and five subgroups and assigned a systematic nomenclature reflecting their positions across the 11 chromosomes. Comprehensive analyses of conserved domains, gene structures and motif features revealed a high degree of conservation with the gene family. Furthermore, seven pairs of segmental and tandem duplication events were detected, suggesting a contribution to the expansion of family. Cis -acting element analysis revealed the presence of hormone-related, stress-related, light-related, and development-related elements in the promoters of the majority of GpWRKY genes. Expression profiling analysis demonstrates that 64 GpWRKY genes were distinct in tissue-specific expression patterns and were substantially induced under Cd stress. Heterologous expression assay confirmed that GpWRKY48 , one of the genes highly induced by Cd, positively regulates Cd tolerance. In this study, GpWRKY genes in G. pentaphyllum for the first time systematically identified and further investigated their physicochemical properties, evolution, and expression patterns, providing a theoretical basis for future studies on the functional characterization of G. pentaphyllum WRKY genes during plant growth and development, as well as Cd stress responses.

Background: Sarcandra glabra , an early-diverging angiosperm of the family Chloranthaceae, is extensively used in traditional medicine and has taxonomic importance. However, the research on the structural information of the complete mitochondrial genome of S . glabra is limited, with no data available for SSR, Ka/Ks ratios, codon analysis, or RNA editing. Results: In this study, we present the complete mitochondrial genome of S . glabra , obtained by high-throughput sequencing using Illumina and Nanopore platforms. It enabled the assembly of a multi-branched genome, consisting of a linear chromosome of 1,120,880 bp and a circular chromosome of 192,931 bp. The annotation identified a total of 81 genes, including 39 protein-coding genes, 21 distinct transfer RNAs with multiple gene copies, and 3 ribosomal RNAs, with an overall GC content of 46.03%. The analysis across 9,547 codons revealed a strong preference for A or U ending codons, and serine was found to be the most common amino acid. A total of 524 RNA editing sites were authenticated via RNA-seq, with the nad5 exhibiting the highest frequency of editing events. Ka/Ks analysis showed that the majority of genes were under purifying selection, while increased ratios in nad4 , cob , and rpl16 implied instances of adaptive evolution. Extensive potential for chromosomal rearrangement was shown by 399 simple sequence repeats and over 3,585 interspersed repetitions, mostly consisting of short forward or palindromic motifs. Phylogenomic analyses of 21 angiosperm mitochondrial genomes placed S . glabra within Chloranthaceae, clustering with Chloranthus spicatus and forming a well-supported sister relationship with Hedyosmum orientale . Conclusions: This work offers the first comprehensive analysis of the S . glabra mitochondrial genome, highlighting its structural complexity, dynamic RNA editing, signatures of adaptive evolution, and its phylogenetic position among basal angiosperms.