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Dendrobium catenatum Lindl (Orchidaceae) has high medicinal and economic value. Unfortunately, industrially-cultivated D. catenatum exhibits inferior medicinal quality in comparison with wild-harvested plant materials. Previously, we produced tetraploid D. catenatum germplasm in order to increase the production of bioactive compounds. However, although tetraploid D. catenatum contains a higher polysaccharide content than diploid D. catenatum , the molecular mechanism is still unknown. In this study, the polysaccharide content of tetraploid D. catenatum stems and leaves was studied alongside a comprehensive transcriptomic and metabolomic analysis. Overall, tetraploid D. catenatum contained a higher polysaccharide content (stem: 30.93%, leaf: 23.28%) than diploid D. catenatum (stem: 17.93%, leaf: 15.28%). Further analyses of differential metabolites and genes were carried out, targeting genes related to polysaccharide synthesis, metabolism, regulation, and transport. Functional enrichment analysis showed that tetraploid plants were highly enriched in transport- and metabolism-related pathways. Specifically, CesA/Csl, SWEET, and BGLU gene family members were upregulated in tetraploid plants. The results of this study suggest that enhanced polysaccharide transport may be the key driver of increased polysaccharide content in tetraploid D. catenatum. These results provide a foundation for further studies aimed at resolving the molecular mechanism of high polysaccharide content in tetraploid D. catenatum , as well as a theoretical basis for the breeding of new D. catenatum varieties. [Display omitted] • The polysaccharide content of Dendrobium catenatum tetraploid stem and leaf tissues was increased as compared to diploid. • Glucose and D-mannose were increased in tetraploids compared to diploids. • Tetraploid plants were highly enriched in transport- and metabolism-related pathways. • The CesA/Csl, SWEET and BGLU gene families may be key drivers of increased polysaccharide content in tetraploids. [ABSTRACT FROM AUTHOR]

Rich flower colors are valuable attributes for Lagerstroemia indica ornamental industry. To gain insights into the regulatory network controlling flower color formation and identify the key regulatory genes, in this study, we comprehensively analyzed the metabolome and transcriptome of three L. indica cultivars at the full bloom stage: red Dynamite, purple Lanmaizi, and white Yuzhuafendie. A total of 111 potential anthocyanin biosynthetic structural genes were screened and assigned among the 24 chromosomes. Significant up-accumulation of cyanidins in cv. Dynamite and petunidins in cv. Lanmaizi confer to them different flower colors. LiANS and LiOMT28 , two structural genes, may work in tandem with transcription factors (TFs) from the MYB, bHLH, WDR, G2-like, ERF, WRKY, bZIP, and E2F/DP families to modulate color formation in L. indica petals, according to correlation tests of anthocyanin levels and transcriptional changes. Subsequent research confirmed the positive correlation between petal colorating processes and the transcripts of LiANS. Increased anthocyanin accumulation in leaves and petals, pale pink flower color, up-regulation of LiF3H1 , LiF3H2 , LiDFR , LiOMT29 , and Lind24G0871 (R2R3 MYB), and down-regulation of Lind04G0622 (R2R3 MYB) were also observed in the LiANS -overexpressing shoots. These findings suggest that LiANS may assemble molecular modules with these structural genes and MYB TFs to participate in anthocyanin biosynthesis in L. indica. Further research on the intricate physiological processes and molecular mechanisms connected to the flower color and its regulatory networks in L. indica may benefit from the novel insights gained from the study. • Cyanidins were enriched in red petals, while petunidins were enriched in purple. • Anthocyanin biosynthetic structural genes were first identified in the L. indica. • LiANS overexpressing changed the petals from white to pale pink hue. [ABSTRACT FROM AUTHOR]

Slash pine (Pinus elliottii) is a crucial resin-tapping tree species in China, and its resin, an important product, is predominantly composed of monoterpenes and diterpenes. Although the influence of transcription factors (TFs) and microRNAs (miRNAs) on terpene biosynthesis is well known, the specific effect of miRNAs on terpene synthesis in slash pine remains insufficiently explored. This study employed comprehensive analyses, including transcriptome sequencing, small RNA sequencing, and degradation profiling, focusing on the bark and needles of slash pine at three distinct time points to unveil the miRNA-gene regulatory patterns governing terpene synthesis. The transcriptome analysis identified 19,673 differentially expressed genes (DEGs), including 726 TF-coding genes, 59 genes related to terpene synthesis, 66 ABC transporter genes, and 317 CYP450 genes. Small RNA sequencing identified 175 miRNAs, with 105 differentially expressed miRNAs (DEMs) targeting 2497 genes. Notably, pta-miR949, pta-miR946a-3p, and pab-miR3710 targeted PITA39236 (HDS), PITA24638 (GPPS), and PITA12789 (ACAT), respectively. Temporal analysis revealed that DEMs and DEGs in Profiles 7 and 13 significantly influenced terpene synthesis in slash pine. Specifically, bHLH genes (Novel9385, PITA08062, PITA23693, and PITA43216) in these expression profiles, as well as the pta-miR858a/b-PITA03784/PITA28059/PITA18794 (MYB) and pta-miR159c-Novel1571/Novel4202 (MYB) modules, play pivotal roles in slash pine terpene synthesis. This study, for the first time, revealed the regulatory role of miRNAs in slash pine terpene synthesis, providing a foundation for understanding the involvement of miRNAs in this process and offering theoretical support for future molecular breeding efforts aimed at enhancing resin yield in slash pine. • pta-miR949-PITA39236 (HDS), pta-miR946a-3p-PITA24638 (GPPS), and pab-miR3710- PITA12789 (ACAT) modules were directly related to the terpene synthesis of slash pine. • bHLH genes (Novel9385, PITA08062, PITA23693, and PITA43216), miR858a/b-PITA03784/PITA28059/PITA18794 module, and pta-miR159c-Novel1571/Novel4202) play pivotal roles in slash pine terpene synthesis. [ABSTRACT FROM AUTHOR]

Ultraviolet‑B (UV-B) is not only a potential environmental stress, but also a kind of pivotal morphogenesis signal. Plants have a variety of coping mechanisms against UV-B stress. We found that long-term UV-B can change the growth phenotype of Betula platyphylla Suk. (birch), increasing the content of lignin, hemicellulose and the cell wall thickness of birch xylem. We analyzed the transcriptome, phosphoproteome, and metabolome of UV-B treated birch. The specific transcriptome response to UV-B in birch was localized to pathways such as phenylpropane and sucrose metabolism. Phosphoproteome reveals that MAPK cascade pathways and multiple CDPKs are activated by UV-B. Through metabolome analysis, we found that the metabolites of the phenylpropane pathway, sucrose pathway, variety of amino acids and lipid metabolism pathway were upregulated under UV-B treatment, and alkaloids were upregulated. We also identified an AP2/ERF transcription factor BpERF11 , which can directly interact with BpMPK3 and phosphorylated in plant and in vitro. BpMPK3 mediated phosphorylation of BpERF11 increases its stability. In conclusion, our study demonstrates that UV-B activates multiple kinase signaling pathways in birch and leads to the accumulation of various secondary metabolites to scavenge reactive oxygen species. This study provides theoretical references for further investigating the molecular mechanisms underlying birch responses to UV-B regulation, laying the foundation for enhancing the adaptability of trees to environmental changes and targeted improvement of wood properties. [Display omitted] • Multi-omics explore the UV-B response mechanism of Betula platyphylla. • Betula platyphylla strengthens the xylem and cell walls to resist UV-B. • MAPK pathway has an essential function in the response of Betula platyphylla to Ultraviolet-B. [ABSTRACT FROM AUTHOR]

Medicinal licorice is obtained from the roots and rhizomes of three species, Glycyrrhiza inflata , G. glabra , and G. urelensis. Previous studies have reported chemical differences among these species, but the detailed composition of specialized metabolites and the underlying molecular basis for the formation of characteristic compounds remain unclear. Here, we performed integrated metabolic and transcriptomic analysis to identify the characteristic flavonoids (CFs) of these three licorice species as well as the key regulators of their biosynthesis. A total of 866 metabolites including 251 flavonoids were identified. Among them, 71 flavonoids were differentially accumulated in three licorice species. Transcriptome analysis showed that a set of the structural genes involved in CF biosynthesis were differentially expressed among the three licorice species. In addition, weighted gene co-expression network analysis (WGCNA) was used to construct a regulatory network for CF biosynthesis. A candidate transcription factor GibHLH69 was proved to promote GiCHS20 expression and contribute to the accumulation of multiple CFs in G. inflata. These results provide valuable information for further understanding the biosynthesis of CFs and future breeding of Glycyrrhiza varieties. • Total 71 characteristic flavonoids (CFs) were identified among three Glycyrrhiza species. • Transcriptome analysis revealed 76 candidate genes related to CF biosynthesis. • A set of transcription factors involved in CF biosynthesis regulation were identified using WGCNA. • GibHLH69 promoted GiCHS20 expression and thus the accumulation of multiple CFs in G. inflata. [ABSTRACT FROM AUTHOR]

Silicon (Si) has the potential to promote plant yield and improve their insect resistance, but the direct defense mechanisms associated with the effects of Si on forage grasses and its regulation are not known. In this study, the conditions of silica fertilization nutrition (1 and 3 mmol L−1 recorded as low concentration (LC) and high concentration (HC) groups, respectively) were changed during the seed germination period, which did not significantly affect the seed germination of ryegrass. However, the shoot biomass and insect resistance of ryegrass were significantly increased in the HC group. Comparison of the transcriptional results from RNA-seq assays revealed that the accumulation of ryegrass biomass may be closely related to the silicon intervention in photosynthesis, and the metabolic synthesis of lignin, carbohydrates, and hemicellulose. There was an additive effect of silicon concentration on the regulatory effects of ryegrass at the transcriptional level. Meanwhile, 98 and 1291 differentially expressed genes were assigned to the metabolic process in the LC and HC groups, respectively. Metabolomic results combined with LC-MS analysis showed that Si initiated a direct defense network in ryegrass with Phenylpropanoid biosynthesis as the backbone, and Flavonoid, Flavone and flavonol, and Isoflavonoid biosynthesis as important branches. The relative content of phenolics was significantly up-regulated, especially in the HC group, and most of these phenolics were potent SOS substances, closely related to the physiological disturbances suffered by Spodoptera frugiperda , with inhibitory effects on larval body weight. The above results confirm that silicon promotes an increase in ryegrass yield while initiating its direct defense network against insects, and that silicon is an effective supplement in improving ryegrass yield and insect resistance. [Display omitted] • Silicon treatment increased the shoot biological production of ryegrass. • Silicon treatment initiated the direct defense network of ryegrass. • Silicon treatment significantly up-regulated the phenolic content in ryegrass. • Silicon treatment improved insect resistance in ryegrass. [ABSTRACT FROM AUTHOR]

Camellia oleifera is an important industrial crop whose leaf, flower, pericarp, and seed have multiple application values. Grafting is the main means of C. oleifera propagation, and the quality of grafted seedlings is directly related to the propagation coefficient and yield promotion. However, the research on C. oleifera grafting is lacking, and there is little comprehensive understanding of the growth characteristics, metabolic patterns, and molecular mechanisms of different grafting combinations of C. oleifera. In this study, the phenotypic, metabolomic, and transcriptomic profiles of four grafting combinations [ C. oleifera (Co), C. yuhsienensis (Cy), C. chekiangoleosa (Cc), and C. gigantocarpa (Cg) four kinds of scions grafted onto one rootstock, C. oleifera (Co)] were investigated. The phenotypic analysis showed that hetero-grafting inhibited the growth vigor of grafted unions. The abundance of shikimic acid and phenylethylamine in hetero-grafting was lower than in auto-grafting based on the differential metabolite analysis, and the exogenous addition of both metabolites promoted the growth of grafted unions. Multi-omics analysis revealed that hetero-grafting could significantly affect the differential expression of hub genes (aroD , aroE , aroK , pheA , tyrB) in the biosynthesis of shikimic acid and phenylethylamine and that AP2/ERF , MYB , and GRAS transcription factors were involved in regulating the expression of the above hub genes. These findings innovatively characterized the important role of shikimic acid and phenethylamine in the growth of C. oleifera grafted seedlings and provided new insights for promoting the propagation and industry development of C. oleifera. [Display omitted] • Hetero-grafting inhibited the growth vigor of Camellia oleifera. • Shikimic acid and phenylethylamine have positive effects on grafted C. oleifera. • The hub genes involved in shikimic acid and phenylethylamine accumulation were screened. • The transcriptional regulation model of the hub genes was established. [ABSTRACT FROM AUTHOR]

Coumarin synthase (COSY) is the key enzyme involved in the coumarin biosynthesis. Although it has been identified firstly in Arabidopisis thaliana , there is little known about the COSY gene function in Clematis terniflora DC. Our previous study indicated that the contents of coumarins in C. terniflora leaf were increased under ultraviolet-B radiation and dark treatments (UV-D). To reveal the function of COSY in C. terniflora and its role in response to UV-D stress, the functional characterization of CtCOSY which was identified as a BADH acyltransferase was performed. The results showed that coupled reaction of CtCOSY with 4-coumarinyl CoA-ligase in vitro to produce umbelliferone. Moreover, the functions of CtCOSY in response to UV-D stress was studied using proteomic and metabolomic techniques. Multi-omics analyses of CtCOSY -silenced C. terniflora indicated that as well as a limitation of coumarin synthesis, aspects of the energy metabolism, such as the TCA cycle, were disturbed in these plants. Under UV-D stress, CtCOSY affected the biosynthesis of phenylpropanoids in C. terniflora , resulting in the improvement of coumarin biosynthesis and affecting purine metabolism. This study provides the evidences of CtCOSY responsible for the biosynthesis of coumarin in C. terniflora and the resistance to UV-D stress. [Display omitted] • Coumarin synthase from Clematis terniflora was firstly characterized. • The energy metabolism pathways were impacted after CtCOSY silenced. • CtCOSY regulated coumarin metabolism pathways under abiotic stress. [ABSTRACT FROM AUTHOR]