Gene Signal Transduction Research Articles

Transcriptomics and Plant Hormone Analysis Reveal the Mechanism of Branching Angle Formation in Tea Plants (Camellia sinensis)

The branching angle of tea plants is a key factor in determining their branching structure, which significantly affects yield, suitability for mechanical harvesting, and overall plant architecture. However, the mechanisms underlying branching angle formation in tea plants remain unclear. In this study, we explored the mechanism of branching angle formation in tea plants by analysing the transcriptome and plant hormone levels of tea plant cultivars with different branching angles. The results indicated that gibberellin positively regulates the branching angle of tea plants, cytokinins, auxin, and abscisic acid involved in the formation of branching angles in tea plants. The transcriptome analysis revealed that candidate regulatory factors, including plant-hormone-related genes (the gibberellin synthesis gene GA3ox1 and metabolism gene GA2ox1; the cytokinin metabolism genes CKX and UGT; the auxin signal transduction-related genes LAX3; and the abscisic acid signal transduction gene PYL4), genes regulating cell division and growth (LAZY1, TAC1, and MAX1), and transcription factors (MYBs, WRKYs, TCPs, AP2/ERFs, and MADS-box), are involved in the formation of branching angles in tea plants. These results offer insights into the mechanism of branching angle formation in tea plants, providing important theoretical reference for the selection and breeding of tea cultivars suitable for mechanical harvesting, thereby improving agricultural efficiency and sustainability.

Growth and physiological response of Yulu Hippophae rhamnoides to drought stress and its omics analysis

ABSTRACT Hippophae rhamnoides (H. rhamnoides) is the primary tree species known for its ecological and economic benefits in arid and semi-arid regions. Understanding the response of H. rhamnoides roots to drought stress is essential for promoting the development of varieties. One-year-old Yulu H. rhamnoides was utilized as the experimental material, and three water gradients were established: control (CK), moderate (T1) and severe (T2), over a period of 120 days. The phenotypic traits and physiological indies were assessed and analyzed, while the roots were subjected by RNA-Seq transcriptome and Tandem Mass Tags (TMT) proteome analysis. Drought stress significantly reduced the plant height, ground diameter, root biomass and superoxide dismutase activity; however, the main root length increased. In comparison with CK, a total of 5789 and 5594 differential genes, as well as 63 and 1012 differential proteins, were identified in T1 and T2, respectively. The combined analysis of transcriptome and proteome showed that the number of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) associated with T1, T2 and CK was 28 and 126, respectively, with 7 and 36 genes achieving effective KEGG annotation. In T1 and T2, the differential genes were significantly enriched in the plant hormone signal transduction pathway, but there was no significant enrichment in the protein expression profile. In T2, 38 plant hormone signal transduction function genes and 10 peroxisome related genes were identified. With the increase of drought stress, the combined expression of DEGs and DEPs increased. Yulu H. rhamnoides may allocate more resources toward CAT while simultaneously decreasing SOD and POD to mitigate the oxidative stress induced by drought. Furthermore, the molecular mechanisms underlying plant hormone signal transduction and peroxisome-related genes in the roots of H. rhamnoides were discussed in greater detail.

Class III peroxidase: An essential enzyme for enhancing plant physiological and developmental process by maintaining the ROS level: A review.

Since plants are sessile organisms, they are inevitably exposed to various environmental stresses, and the accumulation of reactive oxygen species (ROS) could affect the growth and development of plants. ROS play either positive or negative roles in various plant life activities as a two-edge sword. Class III peroxidase (CIII PRX) is a highly conserved antioxidant enzyme family specifically identified in plants, which is involved in maintaining ROS homeostasis in the cell and plays multiple functions in plant growth metabolism and stress response. In this review, the classification and structure of CIII PRXs are represented, and the roles of CIII PRXs in physiological and developmental processes such as plant growth, cell wall modification, loosening and stiffening, and lignin biosynthesis are described in detail. The molecular mechanisms of CIII PRXs in response to abiotic stress such as salt and drought, and biological stress such as pathogens invasion are introduced, with emphasis on the research results of PRX related genes in signal transduction. Furthermore, we summarize the difficulty in exploring the function of individual CIII PRX gene due to functional redundancy and promising technique that may break this research bottleneck.

RNA-seq analysis reveals genes associated with Macrophomina phaseolina-induced host senescence in soybean

BackgroundCharcoal rot of soybean is caused by the hemibiotrophic fungus Macrophomina phaseolina, a global crop destroyer and an important pathogen in the midwestern USA. The quantitative nature of host resistance and the complexity of the soybean-M. phaseolina interaction at the molecular level have hampered resistance breeding. A previous study showed that L-ascorbic acid (LAA) pre-treatment before M. phaseolina inoculation reduced charcoal rot lesion length in excised soybean stems. This study aimed to elucidate the genetic underpinnings of M. phaseolina-induced senescence and the mitigating effects of ascorbic acid on this physiological process within the same pathosystem.ResultsRNA was sequenced from M. phaseolina-resistant and -susceptible soybean genotypes following M. phaseolina inoculation, LAA, and hydrogen peroxide (H2O2)—an oxidative stress inducer—application followed by inoculation. More genes were down-regulated in the resistant and susceptible genotypes than up-regulated when the M. phaseolina-inoculated treatments were compared to mock-inoculated control treatments. Gene ontology (GO) term and KEGG pathways analysis detected M. phaseolina-induced up-regulation of receptor-like kinase genes. In contrast, many genes related to antioxidants, defense, and hormonal pathways were down-regulated in both genotypes. LAA pre-treatment induced genes related to photosynthesis and reactive oxygen species responses in both genotypes. H2O2 pre-treatment following inoculation up-regulated many stress-response genes, while hormone signal transduction and photosynthesis-related genes were down-regulated in both genotypes.ConclusionsResults revealed transcriptional variation and genes associated with M. phaseolina-induced senescence in soybean. Ascorbic acid induced many photosynthetic genes, suggesting a complex regulation of defense and immunity in the plant against the hemibiotroph. Soybean plants also exhibited enhanced stress responsiveness when treated with H2O2 followed by inoculation with M. phaseolina. This study will broaden more research avenues related to transcriptional regulation during the M. phaseolina-soybean interaction and the potential role of receptor-like kinases, oxidative stress-responsive genes, ethylene-mediated signaling and enhanced photosynthetic gene expression when mounting host resistance to this important soybean pathogen.

Leveraging large-scale multi-omics evidences to identify therapeutic targets from genome-wide association studies.

Therapeutic targets supported by genetic evidence from genome-wide association studies (GWAS) show higher probability of success in clinical trials. GWAS is a powerful approach to identify links between genetic variants and phenotypic variation; however, identifying the genes driving associations identified in GWAS remains challenging. Integration of molecular quantitative trait loci (molQTL) such as expression QTL (eQTL) using mendelian randomization (MR) and colocalization analyses can help with the identification of causal genes. Careful interpretation remains warranted because eQTL can affect the expression of multiple genes within the same locus. We used a combination of genomic features that include variant annotation, activity-by-contact maps, MR, and colocalization with molQTL to prioritize causal genes across 4,611 disease GWAS and meta-analyses from biobank studies, namely FinnGen, Estonian Biobank and UK Biobank. Genes identified using this approach are enriched for gold standard causal genes and capture known biological links between disease genetics and biology. In addition, we find that eQTL colocalizing with GWAS are statistically enriched for corresponding disease-relevant tissues. We show that predicted directionality from MR is generally consistent with matched drug mechanism of actions (> 85% for approved drugs). Compared to the nearest gene mapping method, genes supported by multi-omics evidences displayed higher enrichment in approved therapeutic targets (risk ratio 1.75 vs. 2.58 for genes with the highest level of support). Finally, using this approach, we detected anassociation between the IL6 receptor signal transduction gene IL6ST and polymyalgia rheumatica, an indication for which sarilumab, a monoclonal antibody against IL-6, has been recently approved. Combining variant annotation, activity-by-contact maps, and molQTL increases performance to identify causal genes, while informing on directionality which can be translated to successful target identification and drug development.

MdILL6 regulates xylem and vessel development to control internode elongation in spur-type apple.

Spur-type varieties play an important role in facilitating high-density plantings. However, the underlying mechanisms of internode elongation in spur-type varieties are poorly understood. In this research, we investigated the morphological phenotype of annual shoots in four spur-type varieties ('Miyazak', 'Jinfu 18', 'Yanfu No. 6', and 'Liquan spur') and four standard-type varieties ('Aomorifu', 'Shou Fuji', 'Yanfu No. 10', and 'Yanfu No. 3'). Compared with standard-type varieties, spur-type varieties had a shorter shoot length, an average internode length and a smaller xylem size. The content of Jasmonic acid (JA) and Jasmonic acid isoleucine (JA-Ile) significantly increased in spur-type varieties, accompanied by an increase in the expression of JA biosynthesis and signal transduction genes. Exogenous methyl jasmonate (MeJA) inhibited plant height, xylem size, and vessel area. Additionally, we identified an IAA-Leucine Resistant1-like Hydrolase family member, MdILL6, which was highly expressed in spur-type varieties and mature stems. MdILL6 was mainly expressed in the shoot tips and stem, and its protein was located on the endoplasmic reticulum. Overexpression of MdILL6 in apple inhibited plant height and average internode length by decreasing xylem size and vessel area. Our results revealed a molecular mechanism of spur-type variety development affected by the JA pathway and suggest strategies for genetic improvement and regulation of spur-type varieties.

Versatile MXenzymes Scavenging ROS for Promotion of Seed Germination under Salt Stress.

Salinization is recognized as a global problem, restricting agricultural production and sustainability. Targeting the salinity-induced oxidative stress, antioxidant treatment represents a protective strategy to improve plant salt tolerance. Herein, we report a V4C3 MXene nanozyme (MXenzyme), which exhibits good biocompatibility and excellent reactive oxygen species scavenging activity to ameliorate the salt stress-induced inhibition of seed germination. V4C3 MXenzyme treatment can significantly relieve salinity-induced oxidative stress and restore the antioxidant system in pea seeds, thus improving the phenotypic traits during germination. The molecular mechanism by which antioxidant V4C3 MXenzymes augment salt tolerances is revealed through transcriptomics and metabolomics. V4C3 MXenzymes significantly regulate the gene expression of antioxidant enzymes and molecule biosynthesis that correlate closely with hormone signal transduction genes and energy metabolism genes. With correlation and the combined analysis, redox homeostasis targeted by antioxidant V4C3 MXenzymes plays a critical role in promoting plant growth under salt stress.

Analysis of the plant hormone expression profile during somatic embryogenesis induction in teak (Tectona grandis).

Plant somatic embryogenesis (SE) is an efficient regeneration system for propagation. It involves the regulation of a complex molecular regulatory network encompassing endogenous hormone synthesis, metabolism, and signal transduction processes, induced through exogenous plant growth regulators. Previous studies have focused primarily on traditional propagation methods for Tectona grandis, but there is limited knowledge on SE and its hormonal regulatory mechanisms. In our study, different SE stages, including the nonembryogenic callus (NEC), embryogenic callus (EC), and globular and heart-shaped embryo (E-SEs) stages, were induced in teak cotyledons incubated on MS medium supplemented with 0.1 mg/L thidiazuron (TDZ). Morphological and histological observations indicated that EC primarily originates from the development of embryogenic cell clusters. During SE induction, the levels of six classes of endogenous hormones, IAA, CTK, ETH, ABA, SA, and JA, changed significantly. Transcriptome analysis revealed that endogenous hormones participate in SE induction in teak through various biological processes, such as biosynthesis, metabolism, and signal transduction pathways. We found that IAA biosynthesis primarily occurs through the IAM pathway during these three stages. The ETH receptor kinase gene SERF1 exhibited the highest expression levels in E-SEs. The ABA-, SA-, and JA-related signal transduction genes ABI3, NPR1, and JAZ exhibited no differential expression during different stages. Moreover, key encoding genes of SE regulators, including WUS, WOX and SERK, were differentially expressed during SE. In conclusion, this study offers insights into the roles of endogenous hormones and their interactions during SE induction.

Susceptibility of Lymantria dispar to Beauveria bassiana under short-term Cd stress: Humoral immunostimulation cannot offset cellular immunotoxicity

Heavy metal is a serious environmental pollutant with all kinds of biotoxic effects. The immunomodulatory effects of Cd stress on Lymantria dispar larvae and its underlying mechanisms were investigated. The susceptibility of Cd-treated larvae to Beauveria bassiana (Bb) was significantly increased by 27.50 %. The hemocyte count, melanization, encapsulation activities, and expression levels of related regulatory genes (e.g. PPO1 and DSCAM) in the Cd and Cd+Bb groups were markedly lower than those in CK and CK+Bb groups. Hemocyte compensation through the apoptosis inhibitor significantly increased the melanization, encapsulation, and the survival rate of larvae in the Cd+Bb group by 100.00 %, 74.03 %, and 18.33 %, respectively. The expression of signal transduction and effector genes (e.g. Gloverin) was significantly elevated in Cd-treated larvae both before and after Bb infection. Silencing Gloverin resulted in a 9.17 % increase in susceptibility of Cd-treated larvae to Bb. Cd exposure induced humoral immunostimulation in larvae through the CncC-Gloverin pathway, as evidenced by that silencing CncC resulted in a 71.07 % decrease in Gloverin expression and a 19.73 % increase in larval mortality in Cd+Bb group. Overall, the humoral immunostimulation induced by Cd stress in L. dispar larvae were insufficient to counteract the cellular immunotoxicity during Bb infection.

Gibberellins Play an Essential Role in the Bud Growth of Petunia hybrida.

This study delves into the role of gibberellin (GA) in governing plant branch development, a process that remains incompletely understood. Through a combination of exogenous hormone treatment, gene expression analysis, and transgenic phenotype investigations, the impact of GA on petunia's branch development was explored. The results showed that GA3 alone did not directly induce axillary bud germination. However, paclobutrazol (PAC), an inhibitor of GA synthesis, effectively inhibited bud growth. Interestingly, the simultaneous application of GA3 and 6-BA significantly promoted bud growth in both intact and decapitated plants compared to using 6-BA alone. Moreover, this study observed a significant downregulation of GA synthesis genes, including GA20ox1, GA20ox2, GA20ox3, GA3ox1, and CPS1, alongside an upregulation of GA degradation genes such as GA2ox2, GA2ox4, and GA2ox8. The expression of GA signal transduction gene GID1 and GA response factor RGA was found to be upregulated. Notably, the PhGID1 gene, spanning 1029 bp and encoding 342 amino acids, exhibited higher expression in buds and the lowest expression in leaves. The overexpression of PhGID1 in Arabidopsis resulted in a noteworthy rise in the number of branches. This study highlights the crucial role of GA in bud germination and growth and the positive regulatory function of GA signaling in shoot branching processes.

PmLBD3 links auxin and brassinosteroid signalling pathways on dwarfism in Prunus mume

BackgroundGrafting with dwarf rootstock is an efficient method to control plant height in fruit production. However, the molecular mechanism remains unclear. Our previous study showed that plants with Prunus mume (mume) rootstock exhibited a considerable reduction in plant height, internode length, and number of nodes compared with Prunus persica (peach) rootstock. The present study aimed to investigate the mechanism behind the regulation of plant height by mume rootstocks through transcriptomic and metabolomic analyses with two grafting combinations, ‘Longyan/Mume’ and ‘Longyan/Peach’.ResultsThere was a significant decrease in brassinolide levels in plants that were grafted onto mume rootstocks. Plant hormone signal transduction and brassinolide production metabolism gene expression also changed significantly. Flavonoid levels, amino acid and fatty acid metabolites, and energy metabolism in dwarf plants decreased. There was a notable upregulation of PmLBD3 gene expression in plant specimens that were subjected to grafting onto mume rootstocks. Auxin signalling cues promoted PmARF3 transcription, which directly controlled this upregulation. Through its binding to PmBAS1 and PmSAUR36a gene promoters, PmLBD3 promoted endogenous brassinolide inactivation and inhibited cell proliferation.ConclusionsAuxin signalling and brassinolide levels are linked by PmLBD3. Our findings showed that PmLBD3 is a key transcription factor that regulates the balance of hormones through the auxin and brassinolide signalling pathways and causes dwarf plants in stone fruits.

Polyamine oxidase induces flower formation by promoting spermidine and ABA accumulation in cherry (Cerasus pseudocerasus Lindl.)

Polyamines are important small molecules that play a crucial in flower formation in plants. Polyamine oxidases (PAOs) have a significant function in regulating flower development by influencing polyamine homeostasis. Treatment with exogenous Spd resulted in a significant increase in the Spd content in cherry flower buds, which was accompanied by an increase in abscisic acid (ABA) levels and a decrease in gibberellin (GA) levels, as well as a notable rise in the expression of genes associated with flower formation. Polyamine oxidases are essential for maintaining endogenous polyamine homeostasis. Based on the sweet cherry genome and the ‘Manaohong’ cherry transcriptome data, four polyamine metabolism enzyme genes (CpPAO1/2/3/4) were identified. Sequence comparisons of PAO proteins revealed a high degree of sequence similarity between ‘Manaohong’ cherry and sweet cherry, with only a single amino acid variation. Phylogenetic analysis classified CpPAOs into three subclasses. The expression patterns of CpPAOs were significantly tissue-specific, exhibiting higher levels of expression in flowers and young leaves. Exogenous Spd significantly increased the expression abundance of CpPAOs, as well as ABA-related and flower-forming genes. The function of CpPAO2 was subsequently verified through genetic transformation, which demonstrated that the expression levels of ABA synthesis, signal transduction genes, and flower formation genes were substantially elevated in CpPAO2 transgenic lines. These transgenic lines exhibited earlier flowering and a greater number of inflorescences compared to wild type (WT). Yeast single-hybrid and dual-luciferase assays revealed that CpABF5 binds to the promoter of CpSOC1, promoting its expression. Collectively, these results indicated that exogenous Spd increases the content of Spd and Spm while enhancing ABA levels by promoting the transcript level of CpNCEDs in flower buds, thereby facilitating flower formation through the CpABF5-CpSOC1 pathway.

Transcriptomic and metabolomic analysis of quality deterioration of postharvest okra fruit at different storage temperatures

Okra fruit have short postharvest potential and are susceptible to chilling injury (CI). To increase our understanding of the metabolism of okra fruit we have analyzed the transcriptomic and metabolomic changes of the fruit stored at 4, 10, and 22 ℃ for six days. Compared with 0 d, storage at 22 °C for 6 days, senescence and lignification of fruit were associated with upregulation of genes related to abscisic acid (ABA) synthesis and signal transduction (ZEP, NCED, AAO, PYR/PYL, PP2C), lignin synthesis (HCT, 4CL, CCR, CAD, F5H, COMT), and cellulose synthesis (CesA). Chilling injury of okra at 4 ℃ may be caused by the activation of the α-linolenic acid metabolic pathway and flavonoid synthesis pathway, compromised membrane integrity, and higher reactive oxygen species levels. Storage at 10 ℃ resulted in the downregulation of ABA synthesis, signal transduction, and lignin synthesis genes, inhibition of α-linolenic acid pathway metabolites, and the expression of membrane lipid degradation genes (PLD, PLA, lipase, DGK, LOX). Conversely, there was an upregulation of antioxidant enzymes (APX, AO, POD, Grx, MDHAR) and genes involved in the flavonoid synthesis pathway (C4H, CHS, CHI, F3H, ANS), and with their corresponding metabolites (pinocembrin, butin, epiafzelechin, catechin). These changes were associated with slower fruit senescence, indicating that 10 ℃ better maintained the physiological quality of okra fruit after harvest. Based on these findings, a network model was established to control the postharvest quality of okra fruit under different temperature treatments. This study explored the regulatory mechanism of okra at different temperatures at the molecular level and laid a theoretical foundation for improving the quality of postharvest okra and extending its shelf life.

Overexpression of MtIPT gene enhanced drought tolerance and delayed leaf senescence of creeping bentgrass (Agrostis stolonifera L.)

BackgroundIsopentenyltransferases (IPT) serve as crucial rate-limiting enzyme in cytokinin synthesis, playing a vital role in plant growth, development, and resistance to abiotic stress.ResultsCompared to the wild type, transgenic creeping bentgrass exhibited a slower growth rate, heightened drought tolerance, and improved shade tolerance attributed to delayed leaf senescence. Additionally, transgenic plants showed significant increases in antioxidant enzyme levels, chlorophyll content, and soluble sugars. Importantly, this study uncovered that overexpression of the MtIPT gene not only significantly enhanced cytokinin and auxin content but also influenced brassinosteroid level. RNA-seq analysis revealed that differentially expressed genes (DEGs) between transgenic and wild type plants were closely associated with plant hormone signal transduction, steroid biosynthesis, photosynthesis, flavonoid biosynthesis, carotenoid biosynthesis, anthocyanin biosynthesis, oxidation-reduction process, cytokinin metabolism, and wax biosynthesis. And numerous DEGs related to growth, development, and stress tolerance were identified, including cytokinin signal transduction genes (CRE1, B-ARR), antioxidase-related genes (APX2, PEX11, PER1), Photosynthesis-related genes (ATPF1A, PSBQ, PETF), flavonoid synthesis genes (F3H, C12RT1, DFR), wax synthesis gene (MAH1), senescence-associated gene (SAG20), among others.ConclusionThese findings suggest that the MtIPT gene acts as a negative regulator of plant growth and development, while also playing a crucial role in the plant’s response to abiotic stress.

A stage-dependent seed defense response to explain efficient seed transmission of Xanthomonas citri pv. fuscans to common bean.

Although seed represents an important means of plant pathogen dispersion, the seed-pathogen dialogue remains largely unexplored. A multiomic approach was performed at different seed developmental stages of common bean (Phaseolus vulgaris L.) during asymptomatic colonization by Xanthomonas citri pv. fuscans (Xcf), At the early seed developmental stages, we observed high transcriptional changes both in seeds with bacterial recognition and defense signal transduction genes, and in bacteria with up-regulation of the bacterial type 3 secretion system. This high transcriptional activity of defense genes in Xcf-colonized seeds during maturation refutes the widely diffused assumption considering seeds as passive carriers of microbes. At later seed maturation stages, few transcriptome changes indicated a less intense molecular dialogue between the host and the pathogen, but marked by changes in DNA methylation of plant defense genes, in response to Xcf colonization. We showed examples of pathogen-specific DNA methylations in colonized seeds acting as plant defense silencing to repress plant immune response during the germination process. Finally, we propose a novel plant-pathogen interaction model, specific to the seed tissues, highlighting the existence of distinct phases during seed-pathogen interaction with seeds being actively interacting with colonizing pathogens, then both belligerents switching to more passive mode at later stages.

24-epibrassinolide as a multidimensional regulator of rice (Oryza sativa) physiological and molecular responses under isoproturon stress

Brassinosteroids (BRs) can regulate various processes in plant development and defense against environmental stress. In this study, the contribution of BRs in the degradation of isoproturon (IPU) in rice has been established. IPU has a significant effect on rice growth, chlorophyll content, and membrane permeability. When treated with 1.0 μmol/L 24-epibrassinolide (EBR), a BR analogue, the associated symptoms of rice poisoning were alleviated as the IPU levels in the rice and growth media were decreased. In the presence of EBR, the activities of several IPU-related detoxification enzymes were enhanced to cope with the stress due to IPU. An RNA-sequencing (RNA-Seq) has been performed to determine the variation of transcriptomes and metabolic mechanisms in rice treated with EBR, IPU, or IPU+EBR. Some of the differentially expressed genes (DEGs) were Phase I-III reaction components of plants, such as cytochrome P450 (CYP450), glutathione S-transferase (GST), glycosyltransferases (GTs), and the ATP-binding cassette transporter (ABC transporter). The expression of some signal transduction genes was significantly up-regulated. The relative content of low-toxicity IPU metabolites increased due to the presence of EBR as determined by UPLC/Q-TOF-MS/MS. The IPU metabolic pathways include enzyme-catalyzed demethylation, hydroxylation, hydrolysis, glycosylation, and amino acid conjugation processes. The results suggest that EBR plays a key role in the degradation and detoxification of IPU. This study has provided evidence that BRs regulate the metabolism and detoxification of IPU in rice, and offers a new approach to ensuring cleaner crops by eliminating pesticide residues in the environment.

The Molecular Biology Analysis for the Growing and Development of Hydrangea macrophylla ‘Endless Summer’ under Different Light and Temperature Conditions

Hydrangea macrophylla, a celebrated ornamental worldwide, thrives in semi-shaded growth environments in its natural habitat. This study utilizes Hydrangea macrophylla ‘Endless Summer’ as the experimental material to delve into its molecular mechanisms for adapting to semi-shaded conditions. Transcriptome analysis was conducted on leaves from four different natural light growth scenarios, showcasing phenotypic variations. From each sample, we obtained over 276,305,940 clean reads. Following de novo assembly and quantitative assessment, 88,575 unigenes were generated, with an average length of 976 bp. Gene ontology analysis of each control group elucidated the terms associated with the suitable environmental conditions for normal growth, development, and flowering, such as “reproductive bud system development” and “signal transduction”. The exploration of gene interactions and the identification of key genes with strong connectivity were achieved by constructing a protein–protein interaction (PPI) network. The results indicate that hydrangea grows vigorously and blooms steadily under semi-shaded conditions; the photosynthetic efficiency of hydrangea is stabilized through genes related to photosynthesis, such as PHYB, PSBR, FDC, etc. Hormone signal transduction genes like PIN3, LAX2, TIF6B, and EIN3 play important roles in responding to environmental stimulation and regulating growth and development, while genes such as SOC1, COL4/5/16, and AGL24 promote flowering. The expression of genes such as BGLUs and TPSs provides additional energy substances to support flowering.

Comparative transcriptomic analysis revealed important processes underlying the static magnetic field effects on Arabidopsis.

Static magnetic field (SMF) plays important roles in various biological processes of many organisms including plants, though the molecular mechanism remains largely unclear. Here in this study, we evaluated different magnetic setups to test their effects on growth and development on Arabidopsis (Arabidopsis thaliana), and discovered that plant growth was significantly enhanced by inhomogeneous SMF generated by a regular triangular prism magnet perpendicular to the direction of gravity. Comparative transcriptomic analysis revealed that auxin synthesis and signal transduction genes were upregulated by SMF exposure. SMF also facilitated plants to maintain the iron homeostasis. The expression of iron metabolism-related genes was downregulated by SMF, however, the iron content in plant tissues remains relatively unchanged. Furthermore, SMF exposure also helped the plants to reduce ROS level and synergistically maintain the oxidant balance by enhanced activity of antioxidant enzymes and accumulation of nicotinamide. Taken together, our data suggested that SMF is involved in regulating the growth and development of Arabidopsis thaliana through maintaining iron homeostasis and balancing oxidative stress, which could be beneficial for plant survival and growth. The work presented here would extend our understanding of the mechanism and the regulatory network of how magnetic field affects the plant growth, which would provide insights into the development of novel plant synthetic biology technologies to engineer stress-resistant and high-yielding crops.

Regulatory microRNAs and phasiRNAs of paclitaxel biosynthesis in Taxus chinensis.

Paclitaxel (trade name Taxol) is a rare diterpenoid with anticancer activity isolated from Taxus. At present, paclitaxel is mainly produced by the semi-synthetic method using extract of Taxus tissues as raw materials. The studies of regulatory mechanisms in paclitaxel biosynthesis would promote the production of paclitaxel through tissue/cell culture approaches. Here, we systematically identified 990 transcription factors (TFs), 460 microRNAs (miRNAs), and 160 phased small interfering RNAs (phasiRNAs) in Taxus chinensis to explore their interactions and potential roles in regulation of paclitaxel synthesis. The expression levels of enzyme genes in cone and root were higher than those in leaf and bark. Nearly all enzyme genes in the paclitaxel synthesis pathway were significantly up-regulated after jasmonate treatment, except for GGPPS and CoA Ligase. The expression level of enzyme genes located in the latter steps of the synthesis pathway was significantly higher in female barks than in male. Regulatory TFs were inferred through co-expression network analysis, resulting in the identification of TFs from diverse families including MYB and AP2. Genes with ADP binding and copper ion binding functions were overrepresented in targets of miRNA genes. The miRNA targets were mainly enriched with genes in plant hormone signal transduction, mRNA surveillance pathway, cell cycle and DNA replication. Genes in oxidoreductase activity, protein-disulfide reductase activity were enriched in targets of phasiRNAs. Regulatory networks were further constructed including components of enzyme genes, TFs, miRNAs, and phasiRNAs. The hierarchical regulation of paclitaxel production by miRNAs and phasiRNAs indicates a robust regulation at post-transcriptional level. Our study on transcriptional and posttranscriptional regulation of paclitaxel synthesis provides clues for enhancing paclitaxel production using synthetic biology technology.

Transcriptome Analysis Revealed the Possible Reasons for the Change of Ni Resistance in Rhus typhina after Spraying Melatonin.

Melatonin (MT) plays an important role in alleviating the stress of soil heavy metal pollution on plants. However, its ability to improve the tolerance of Rhus typhina to Ni stress and its mechanism of action are still unclear. Therefore, MT (0, 50, 100, and 200 μmol·L-1) was sprayed on the leaf surface of R. typhina seedlings under Ni (0 and 250 mg·kg-1) stress to study the differences in growth, physiology, and gene expression. The results showed that exogenous MT could improve the ability of R. typhina to resist Ni stress by inhibiting the degradation of chlorophyll and carotenoid, enhancing photosynthesis, and augmenting the activity of antioxidant enzymes. Moreover, 100 μmol·L-1 MT could increase the Ni concentration in R. typhina seedlings and reduce the translocation factor. Transcriptome analysis showed that MT mainly regulated the expression of related genes in plant hormone signal transduction, starch and sucrose metabolism, and various amino acid metabolism pathways. This study combined physiological and transcriptomic analysis to reveal the molecular mechanism of MT enhancing Ni resistance in R. typhina, and provides a new direction for expanding its application in phytoremediation.