Sucrose Metabolism Research Articles

Comparative miRNAome combined with transcriptome and degradome analysis reveals a novel miRNA-mRNA regulatory network associated with starch metabolism affecting pre-harvest sprouting resistance in wheat.

Pre-harvest sprouting (PHS) is one of the most important problems associated with the severe decrease of yield and quality under disaster weather of continuous rain in wheat harvesting stage. At present, the functions and mechanisms related to the involvement of post-transcriptional regulation has not been studied very clearly in PHS resistance. This study compared the differences of germinated seeds in miRNAome between the PHS-tolerant and PHS-susceptible white wheat varieties. A total of 1879 miRNAs were identified from three different stages during seed germination. In order to further obtain candidate miRNAs, the different datasets of differentially expressed miRNAs were excavated by using differential-expression and time-series analysis. Combined with degradome data, the miRNA-mRNA networks analysis was performed after genome-wide screening of target genes, and then KEGG enrichment highlighted that the starch and sucrose metabolism pathway related to PHS was specifically enriched in an especial target-gene dataset derived from R12R18-HE miRNAs. Based on transcriptome data, a network associated with starch metabolism was systematically and completely reconstructed in wheat. Then, the starch degradation pathway controlled by seven miRNA-RNA pairs were supposed to be the essential regulation center for seed germination in wheat, which also could play a critical role on the PHS resistance. Our findings revealed the complex impact of the miRNA-mediated mechanism for forming intrinsic and inherent differences, which resulting in significant difference on PHS performance between white wheat varieties.

Effects of rumen-degradable starch on lactation performance, gastrointestinal fermentation, and plasma metabolomic in dairy cows.

This study investigated the effects of rumen-degradable starch (RDS) on lactation performance, gastrointestinal fermentation, and plasma metabolomics in dairy cows. Six mid-lactation cows, fitted with rumen, duodenum, and ileum cannulas, were used in a duplicated 3 × 3 Latin square design with 28-day periods. The cows were fed a low RDS (LRDS; 62.18 %), medium-RDS (MRDS; 71.25 %), or high-RDS (HRDS; 80.32 %) diet. The results showed that cows fed HRDS had diet a lower milk fat content by 14.77 % (LRDS) and 11.73 % (MRDS), while increased somatic cell count compared to the LRDS and MRDS groups (34.42 and 29.38 %, respectively). Additionally, rumen fluid pH was decreased in the HRDS group than in the MRDS and LRDS groups (7.81 and 7.08 %, respectively), while microbial protein (MCP) concentration was higher in the MRDS group. The HRDS group had lower concentrations of total volatile fatty acids (TVFA) and acetate in the ileal digesta than the LRDS group. The HRDS diet decreased neutral detergent fibre (NDF) digestibility compared with LRDS and MRDS groups (7.68 and 8.50 %, respectively), and reduced plasma concentrations of superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX), while increasing plasma lipopolysaccharide (LPS) and serum amyloid-A (SAA) levels. Pathway analysis revealed that starch and sucrose metabolism, galactose metabolism, and carbohydrate digestion and absorption were upregulated in the MRDS and HRDS groups. The HRDS diet had a tendency to negatively affect linoleic acid metabolism, glycerophospholipid metabolism, and alpha-linolenic acid metabolism. These findings provide insights into optimising feed efficiency and milk quality by regulating RDS levels in dairy cow diets.

Correlation analysis of transcriptome and metabolomics and functional study of Galactinol synthase gene (VcGolS3) of blueberry under salt stress.

Soil salinity poses a significant environmental challenge for the growth and development of blueberries. However, the specific mechanisms by which blueberries respond to salt stress are still not fully understood. Here, we employed a comprehensive approach integrating physiological, metabolomic, and transcriptomic analyses to identify key metabolic pathways in blueberries under salt stress. Our findings indicate that blueberries primarily adapt to salt stress by modulating pathways associated with carbohydrate metabolism, organic acid metabolism, amino acid metabolism, and various organic compounds. Key metabolites involved in this response include sucrose, propionic acid, and palmitic acid. A total of 241 transcription factors were differentially expressed, with significant involvement from families such as AP2, Dof, GATA, WRKY, and TCP. Notably, the galactose metabolism pathway was associated with 5 DAMs and 24 DEGs, while the starch and sucrose metabolism pathway contained 5 DAMs and 23 DEGs, highlighting their crucial roles in mitigating salt stress. Overexpression of VcGolS3 in transgenic Arabidopsis conferred tolerance to salt and drought stresses, primarily evidenced by a significant increase in GolS enzyme activity and reduced ROS accumulation. This study provides valuable insights into the molecular mechanisms underlying the blueberry response to salt stress and lays the groundwork for breeding salt- and drought-tolerant blueberry varieties.

Transcriptome Reveals the Differential Regulation of Sugar Metabolism to Saline-Alkali Stress in Different Resistant Oats.

Saline-alkali stress is a major factor limiting the growth of oats. Sugar is the primary carbon and energy source in plants which regulates plant development and growth by regulating enzyme activity and gene expression. Sucrose, glucose, and fructose are ubiquitous plant-soluble sugars that act as signalling molecules in the transcriptional regulation of various metabolic and defence-related genes. In this study, soluble sugars, fructose, sucrose, and starch contents were measured, and transcriptomics was used to determine the differentially expressed genes (DEGs) in saline-sensitive and saline-tolerant oats after 6, 12, 24, and 48 h. DEGs annotated to carbohydrates were selected using the Kyoto Encyclopedia of Genes and Genomes. DEGs involved in carbohydrate metabolism were mainly enriched in the glycolysis/gluconeogenesis and pentose phosphate pathways, fructose and mannose metabolism, and starch and sucrose metabolism. GAPDH, SUPI, SUS2, ATP-PEK, HXK6, FBA4, TBA4, TKT, ISA3, PPDK1, and BAM2 were significantly expressed, and a quantitative reverse transcription polymerase chain reaction verified the transcriptome sequencing results. In this study, oats with different salinity tolerances were used to determine sugar contents under four salinity stress durations, and transcriptome sequencing was used to explore the regulatory mechanism of sugars and provide a reference for elucidating the sugar signalling regulatory mechanism under abiotic stress.

Hormesis effect of cadmium on pakchoi growth: Unraveling the ROS-mediated IAA-sugar metabolism from multi-omics perspective.

Previous research on cadmium (Cd) focused on toxicity, neglecting hormesis and its mechanisms. In this study, pakchoi seedlings exposed to varying soil Cd concentrations (CK, 5, 10, 20, 40 mg/kg) showed an inverted U-shaped growth trend (hormesis characteristics): As Cd concentration increases, biomass exhibited hormesis character (Cd5) and then disappear (Cd40). ROS levels rose in both Cd treatments, with Cd5 being intermediate between CK and Cd40. But Cd5 preserved cellular structure, unlike damaged Cd40, hinting ROS in Cd5 acted as signaling regulators. To clarify ROS controlled subsequent metabolic processes, a multi-omics study was conducted. The results revealed 143 DEGs and 793 DEMs across all Cd treatment. KEGG indicated among all Cd treatments, the functional differences encompass: "plant hormone signal transduction" and "starch and sucrose metabolism". Through further analysis, we found that under the influence of ROS, the expression of IAA synthesis and signaling-related genes was significantly up-regulated, especially under Cd5 treatment. This further facilitated the accumulation of reducing sugars, which provided more energy for plant growth. Our research results demonstrated the signaling pathway involving ROS-IAA-Sugar metabolism, thereby providing a novel theoretical basis for cultivating more heavy metal hyperaccumulator crops and achieving phytoremediation of contaminated soils.

Molecular Mechanisms of Grain Chalkiness Variation in Rice Panicles.

Grain chalkiness adversely affects rice quality, and the positional variation of grain chalkiness within a rice panicle presents a substantial obstacle to quality improvement in China. However, the molecular mechanism underlying this variation is unclear. This study conducted a genetic and physiological analysis of grains situated at distinct positions (upper, middle, and bottom primary branches of the rice panicle, denoted as Y1, Y2, and Y3) within a rice panicle using the Yangdao 6 variety. The results indicated that the percentage of chalky grains (PCG) in Y1 was the highest, i.e., 17.12% and 52.18% higher than that of Y2 and Y3, respectively. Y2 exhibited the highest degree of grain chalkiness (DGC), attributable to its greater area of endosperm chalkiness (AEC) than the others. Y3 demonstrated the lowest PCG and DGC. Additionally, Y1 and Y2 were characterized by lower amylose and protein contents, as well as looser starch granule morphology, in comparison to Y3. Compared with Y3, both the average and maximum filling rates of Y1 and Y2 increased markedly; however, the active filling duration was notably reduced by 7.10 d and 5.56 d, respectively. The analysis of genomic expression levels indicated an enrichment of starch and sucrose metabolism in Y1-vs.-Y2, Y2-vs.-Y3, and Y1-vs.-Y3, with 7 genes (5 up-regulated and 2 down-regulated), 53 genes (12 up-regulated and 41 down-regulated), and 12 genes (2 up-regulated and 10 down-regulated) in the Y1-vs.-Y2, Y2-vs.-Y3, and Y1-vs.-Y3. The majority of these genes were down-regulated, linking metabolic activity to grain filling and contributing to the occurrence of grain chalkiness in rice panicles. In conclusion, the metabolic processes associated with sucrose and starch play a crucial role in regulating grain filling and the formation of chalkiness in rice.

Physiological and transcriptomic analysis of the effect of overexpression of the NTPIP2;4 gene on drought tolerance in tobacco

Aquaporins are widely present in the plant kingdom and play important roles in plant response to abiotic adversity stresses such as water and temperature extremes. In this study, we investigated the regulatory role of NTPIP2;4 on drought tolerance in tobacco at physiological and transcriptional levels. In this experiment, we constructed an NtPIP2;4 overexpression vector and genetically transformed tobacco variety 'K326' to investigate the mechanism of NtPIP2;4 gene in regulating drought tolerance in tobacco at physiological and transcriptomic levels. Physiological analyses showed that overexpression plants showed low wilting under drought conditions compared to wild-type (WT), and NtPIP2;4 overexpression tobacco plants showed enhanced superoxide dismutase (SOD) and catalase (CAT) activities, lower levels of superoxide anion (O2-), malondialdehyde (MDA), and hydrogen peroxide (H2O2) than the control, and significantly higher proline (Pro) content than the control. The leaves of NtPIP2;4 overexpressing plants and wild-type controls after drought were subjected to transcriptome sequencing, and RNA-seq analysis showed that a total of 1752 differentially expressed genes (DEGs) were obtained under drought conditions, with 1005 DEGs of up-regulated and 747 DEGs of down-regulated differentially expressed genes. The DEGs were enriched mainly in the plant MAPK signaling pathway, the plant hormone signal transduction pathway, amino sugar and nucleotide sugar metabolism, starch and sucrose metabolism and plant-pathogen interaction pathways. We also investigated the drought pathway of MAPK pathway and the auxin pathway mechanism of plant hormone signal transduction pathway, and found that the transcript levels of the genes of the relevant pathways changed, and hypothesized that NtPIP2;4 might regulate the drought resistance of plants through the expression of the relevant genes induced by auxin. This study demonstrates that overexpression of NtPIP2;4 gene can enhance the drought resistance of tobacco plants, which will provide a basis for the research on the function of tobacco NtPIP2;4 gene and the creation of new germplasm resources.

Chemical Diversity of UK-Grown Tea Explored Using Metabolomics and Machine Learning.

Dartmoor Estate Tea plantation in Devon, UK, is renowned for its unique microclimate and varied soil conditions, which contribute to the distinctive flavours and chemical profiles of tea. The chemical diversity of fresh leaf samples from various garden locations was explored within the plantation. Fresh leaf, which differed by location, cultivar, time of day, and variety, was analysed using Flow Infusion Electrospray Ionisation Mass Spectrometry (FIE-MS). Random forest classification revealed no significant differences between Georgian N2 cultivar garden locations. However, a significant degree of variability was observed within four tri-clonal variants (Tocklai Variety) with TV9 exhibiting greater similarity to the Georgian N2 cultivar compared to TV8 and TV11, while TV11 was found to be most like TV1. The intraclass variability in leaf composition was similar between the varieties. We explored the metabolic changes over the day in one variant (Camellia assamica Masters), yielding a model with a significant R2 value of 0.617 (p < 0.01, 3000 permutations). Starch and sucrose metabolism was found to be significant where the abundance of these chemical features increased throughout the day and then began to decrease at night. This research highlights the complex interplay of cultivars, geographical location, and temporal factors on the chemical composition of tea. It provides insightful data on the metabolic pathways influencing tea cultivation and production and underscores the importance of these variables in determining the final chemical profile and organoleptic characteristics of tea products.

Biochemical, Histological, and Multi-Omics Analyses Reveal the Molecular and Metabolic Mechanisms of Cold Stress Response in the Chinese Soft-Shelled Turtle (Pelodiscus sinensis).

The Chinese soft-shelled turtle (Pelodiscus sinensis), a type of warm-water reptile, is frequently chosen as the model animal to understand how organisms respond to environmental stressors. However, the responsive mechanism of P. sinensis to natural cold stress is unclear, especially in terms of metabolic pattern and molecular pathways. Herein, plasma biochemical, hepatic morphological, apoptotic, transcriptomic, and metabolomic detection methods were performed to investigate the response of P. sinensis to acute cold stress. A consistent increase in plasma AST and ALT activities with a decline in ALP activity was found following 14 °C and 7 °C cold stress compared with the control group. Plasma GLU, TG, CHO, and HDL contents, reflecting energy metabolism, were decreased to lower levels from 2 to 16 days post cold stress (dps). Histological and TUNEL detection in the liver demonstrated that the 14 °C and 7 °C cold stress caused severe morphological damage and cell apoptosis in a time-dependent manner. DEGs in the biosynthesis of fatty acids (Acsbg2, Acsl3, Acsl4, Acsl5, Mcat, and Acacb), as well as unsaturated fatty acids (Hsd17b12, Elovl7, Scd, and Baat), starch and sucrose metabolism (Pgm1, Pgm2, and Treh), and apoptosis (Ddit3, Gadd45a, Lmnb1, Tuba1c, Tnf, Tnfsf10, Fos, Itpr1, and Ctso) were discovered in the transcriptome under cold stress. The metabolomic data showed that metabolites, including chenodeoxycholic acid, oleoylethanolamide, uric acid, fructose 1,6-bisphosphate, CMP, and S-(Hydroxymethyl)-glutathione, were remarkably altered in the cold stress groups. Combined transcriptomic and metabolomic data revealed that pyrimidine metabolism, amino acid metabolism, and pyruvate metabolism were the most significant pathways regulated by the low-temperature exposure. Overall, this work suggests that 14 °C and 7 °C cold stress could induce obvious morphological damage and apoptosis in the liver at 4 dps. Moreover, energy metabolism and amino acid metabolism were the main signaling pathways in response to cold stress for P. sinensis.

Exogenous 24-Epibrassinolide Improves Low-Temperature Tolerance of Maize Seedlings by Influencing Sugar Signaling and Metabolism.

Low-temperature (LT) stress seriously affects the distribution, seedling survival, and grain yield of maize. At the seedling emergence stage, maize's coleoptile is one of the most sensitive organs in sensing LT signaling and, in general, it can envelop young leaves to protect them from LT damage. In addition, brassinolides (BRs) have been shown to enhance LT tolerance from various species, but the effects of BRs on coleoptiles in maize seedlings under LT stress are unclear. Therefore, in this study, the pre-cultured coleoptiles of Zheng58 seedlings were treated with or without 2.0 μM 24-epibrassinolide (EBR) at 25 °C and 10 °C environments for five days to analyze their physiological and transcriptomic changes. Physiological analysis showed that a 10°C LT stress increased the content of glucose (0.43 mg g-1 FW), sucrose (0.45 mg g-1 FW), and starch (0.76 mg g-1 FW) of Zheng58 coleoptiles compared to a 25°C environment. After the coleoptiles were exposed to a 2.0 μM EBR application under 10°C temperature for five days, the contents of these three sugars continued to increase, and reached 2.68 mg g-1 FW, 4.64 mg g-1 FW, and 9.27 mg g-1 FW, respectively, indicating that sugar signaling and metabolism played key roles in regulating LT tolerance in the coleoptiles of maize seedlings. Meanwhile, a transcriptome analysis showed that 84 and 15 differentially expressed genes (DEGs) were enriched in the sucrose and starch metabolism and photosynthesis pathways, respectively, and multiple DEGs involved in these pathways were significantly up-regulated under LT stress and EBR stimulation. Further analysis speculated that the four DEGs responsible for sucrose-phosphate synthetase (SPS, i.e., Zm00001d048979, probable sucrose-phosphate synthase 5 and Zm00001d012036, sucrose-phosphate synthase 1), sucrose synthase (SUS, Zm00001d029091, sucrose synthase 2 and Zm00001d029087, sucrose synthase 4) were crucial nodes that could potentially link photosynthesis and other unknown pathways to form the complex interaction networks of maize LT tolerance. In conclusion, our findings provide new insights into the molecular mechanisms of exogenous EBR in enhancing LT tolerance of maize seedlings and identified potential candidate genes to be used for LT tolerance breeding in maize.

Metabolic and transcriptional analysis of tuber expansion in Curcuma kwangsiensis

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.

Dynamic changes in primary and secondary metabolites of monascal brown rice through γ-aminobutyric acid microcapsule supplementation and untargeted metabolomic analysis

Abstract This study aimed to study the effect of modification of monascal brown rice (MBR) solid-state fermentation through supplementation of γ-aminobutyric acid (GABA) microcapsules from the emulsification/internal gelation technique on dynamic changes in primary and secondary metabolites during 25-day fermentation to conduct metabolomic analysis. During MBR fermentation, the d50 values of GABA microcapsules increased due to their swelling during the MBR fermentation. The lowest encapsulation efficiency (EE%) and highest cumulative release (CR%) of GABA microcapsules found after 25 days of the fermentation were 40.18% and 89.13%, respectively. It was an interesting point that supplementation of microencapsulated GABA into MBR substrate could expand the stationary phase (days 10–20 of the fermentation) of M. purpureus growth curve compared to the control (days 10–15 of the fermentation). During the stationary phase, the concentrations of alanine, phenylalanine, arginine, tyrosine, and tryptophan in MBR fermentation with GABA microcapsule supplementation rose by more than 1.2-fold relative to the control, whereas linolenic acid, linoleic acid, and oleic acid demonstrated increases of over 1.24, 1.31, and 1.42-fold, respectively. Following a 25-day fermentation period, the maximum concentration of GABA detected in the MBR supplemented with GABA microcapsules was 1,267.13 mg/kg, in comparison to the control. Considering HCA and variable importance in projection (VIP), the primary metabolites MBR from GABA microcapsule supplementation positively correlated with days 10 and 15 of the fermentation but days 20 and 25 of the fermentation for the secondary metabolites. The significant metabolic pathways based on the primary and secondary metabolites of MBR from GABA microcapsule supplementation were 1. starch and sucrose metabolism, 2. neomycin, kanamycin, and gentamicin biosynthesis, 3. biosynthesis of unsaturated fatty acids, 4. phenylalanine, tyrosine, and tryptophan biosynthesis, 5. arginine and proline metabolism, 6. citrate cycle (TCA cycle), 7. fructose and mannose metabolism, and 8. pyruvate metabolism.

Non-Additive Gene Expression in Carbon and Nitrogen Metabolism Drives Growth Heterosis in Populus deltoides.

Growth heterosis is crucial for Populus deltoides breeding, a key industrial-timber and ecological-construction tree species in temperate regions. However, the molecular mechanisms underlying carbon (C)-nitrogen (N) metabolism coordination in regulating growth heterosis remain unclear. Herein high-hybrids of P. deltoides exhibited high-parent heterosis and mid-parent heterosis in growth traits and key enzymes of C-N metabolism. In hybrids, gene expression patterns were mainly biased toward female parent. Parental contribution to growth heterosis in P. deltoides is differentiation, rather than absolute maternal or paternal dominance contributions. Parental genes were predominantly and dynamically inherited in a non-additive manner, mainly with dominant expression patterns. A total of 44 non-additive genes associated with photosynthetic C fixation, starch and sucrose metabolism, sucrose transport, photorespiration, and nitrogen metabolism coregulated growth heterosis by coordinating C-N metabolism. Growth-regulating factors 4 interacted with DELLA genes to promote growth by enhancing this coordination. Additionally, five critical genes were identified. Briefly, the above genes in high-hybrids improved photosynthesis and N utilisation by regulating carbohydrate accumulation and enzyme activity, while reducing respiratory energy consumption, thereby providing more energy for growth and promoting growth heterosis. Our findings offer new insights and theoretical basis for deep understanding genetic and molecular regulation mechanisms of tree heterosis and its application in precision hybrid breeding.

Transcriptome Analysis Revealed the Molecular Mechanism of Acetic Acid Increasing Monascus Pigment Production in Monascus ruber CICC41233.

The addition of acetic acid to Monascus ruber cultures is usually used to inhibit the growth of heterotrophic bacteria; however, we found that acetic acid also promotes the growth of M. ruber CICC41233, as well as the synthesis of Monascus pigments (MPs). Compared with no acetic acid or HCl addition, the diameter of M. ruber CICC41233 colonies increased significantly under acetic acid conditions. On the sixth day of fermentation, the yield of total pigments in M. ruber increased significantly by 9.97 times (compared with no acetic acid) and 13.9 times (compared with hydrochloric acid). The transcriptomics data showed that the differentially expressed genes between M. ruber with acetic acid and without acetic acid were mainly involved in starch and sucrose metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, TCA cycle, and oxidative phosphorylation, and that these differentially expressed genes were not involved in amino acid metabolism. Gene expression analysis showed that the relative expression levels of MP synthesis genes (MpPKS5, MppA, MpFasB, MppB, MppD, and MppR2) were significantly up-regulated under acetic acid conditions. This study clarified the metabolic mechanism of acetic acid promoting the growth of M. ruber and the synthesis of MPs, which provided some theoretical guidance for the large-scale production of MPs in the industry in future.

Comparative transcriptome and metabolome analysis of sweet potato (Ipomoea batatas (L.) Lam.) tuber development.

Sweet potato is an important food, feed and industrial raw material, and its tubers are rich in starch, carotenoids and anthocyanins. To elucidate the gene expression regulation and metabolic characteristics during the development of sweet potato tubers, transcriptomic and metabolomic analyses were performed on the tubers of three different sweet potato varieties at three developmental stages (70, 100, and 130 days (d)). RNA-seq analysis revealed that 16,303 differentially expressed genes (DEGs) were divided into 12 clusters according to their expression patterns, and the pathways of each cluster were annotated. A total of 9118 DEGs were divided into three categories during the same developmental period. A total of 1566 metabolites were detected, which were mainly divided into 12 categories. DEGs and differentially regulated metabolites (DRMs) were significantly enriched in the starch and sucrose metabolism and flavonoid biosynthesis pathways. The DEGs associated with the flavonoid pathway showed greater expression with the development of tubers, with the highest expression occurring at 130 d; chalcone isomerase (CHI) was a key gene associated with 11 flavonoid compounds. The DEGs associated with the starch pathway presented relatively low expression during the development of tubers, with the highest expression occurring at 70 d; UDP-glucose pyrophosphorylase 2 (UPG2) and glycogen synthase (glgA) were able to regulate the key genes of 8 metabolites related to the starch biosynthesis pathway. The anthocyanin content is directly related to changes in the content of peonidin-3-O-(6"-O-feruloyl)sophoroside-5-O-glucoside, which is regulated by the IbCHI gene. The abundance of this starch is directly related to changes in the content of D-glucose 6-phosphate and is regulated by the IbUGP2 and IbglgA genes. A total of 14 candidate genes related to starch, carotenoids and anthocyanins in sweet potato tubers, including the IbCHI, IbUGP2 and IbglgA genes, were identified via weighted correlation network analysis (WGCNA). This research provides fresh insights into the levels of anthocyanins, starch, and carotenoids throughout the growth of sweet potato tubers and sheds light on the potential regulatory pathways and candidate genes involved in this developmental progression.

Metabolome–transcriptome association analysis revealed the candidate gene involved in soluble sugar content regulation in cucumber fruits

Soluble sugar content is a crucial parameter affecting the taste and flavor of cucumber. Fruit sweetness varies depending on the soluble sugar content. To explore the regulatory mechanism underlying soluble sugar content, we performed metabolome sequencing on diploid (low soluble sugar, CK) and autotetraploid (high soluble sugar, T) cucumber fruits on the day of flowering (S1) and 9 days after flowering (S2). Metabolome sequencing was combined with corresponding transcriptome analysis. In total, 250 and 387 differential metabolites were screened at S1 (T_S1 vs CK_S1) and S2 (T_S2 vs CK_S2), respectively. The combined analysis unveiled that the differentially expressed genes were primarily concentrated in the pathways of starch and sucrose metabolism and galactose metabolism, among others. Overall, 16 differentially expressed genes and three differential metabolites, including sucrose, stachyose, and trehalose, were identified. Csa_5G322500 expressed abundantly and in large differential multiples, as evident from the transcriptome data of diploid and tetraploid cucumber fruits at different developmental stages, indicating that Csa_5G322500 may be the key gene affecting the soluble sugar content of fruits. Agrobacterium-mediated transformation of the plants with Csa_5G322500 revealed significant increases in the soluble sugar content of cucumber at 24, 36, and 48 h after Agrobacterium infection and a significant increase in the expression of Csa_5G322500 at 36 and 48 h after infection. In conclusion, Csa_5G322500 is potentially involved in regulating the soluble sugar content regulation in cucumber fruits.

Identifying Candidate Genes Related to Soybean (Glycine max) Seed Coat Color via RNA-Seq and Coexpression Network Analysis.

The quality of soybeans is reflected in the seed coat color, which indicates soybean quality and commercial value. Researchers have identified genes related to seed coat color in various plants. However, research on the regulation of genes related to seed coat color in soybeans is rare. In this study, four lines of seed coats with different colors (medium yellow 14, black, green, and brown) were selected from the F2:5 population, with Beinong 108 as the female parent and green bean as the male parent, and the dynamic changes in the anthocyanins in the seed coat were stained with 4-dimethylaminocinnamaldehyde (DMACA) during the grain maturation process (20 days from grain drum to seed harvest). Through RNA-seq of soybean lines with four different colored seed coats at 30 and 50 days after seeding, we can further understand the key pathways and gene regulation modules between soybean seed coats of different colors. DMACA revealed that black seed coat soybeans produce anthocyanins first and have the deepest staining. Clustering and principal component analysis (PCA) of the RNA-seq data divided the eight samples into two groups, resulting in 16,456 DEGs, including 5359 TFs. GO and KEGG enrichment analyses revealed that the flavonoid biosynthesis, starch and sucrose metabolism, carotenoid biosynthesis, and circadian rhythm pathways were significantly enriched. We also conducted statistical and expression pattern analyses on the differentially expressed transcription factors. Based on weighted gene coexpression network analysis (WGCNA), we identified seven specific modules that were significantly related to the four soybean lines with different seed coat colors. The connectivity and functional annotation of genes within the modules were calculated, and 21 candidate genes related to soybean seed coat color were identified, including six transcription factor (TF) genes and three flavonoid pathway genes. These findings provide a theoretical basis for an in-depth understanding of the molecular mechanisms underlying differences in soybean seed coat color and provide new genetic resources.

Proteomics and transcriptomic analyses provide new insights into the pectin polysaccharide biosynthesis in Premna puberula Pamp

Premna puberula Pamp. is a plant with similarities to both food and medicine, which has attracted the attention of researchers because of the rich pectin in its leaves. However, the mechanism of efficient pectin accumulation remains unclear. Through transcriptomic and proteomic analyses, this study investigated the differentially expressed genes and proteins associated with pectin during various developmental stages of P. puberula. The combined omics approach revealed that the majority of differential genes are mainly involved in the anabolic metabolism of primary and secondary metabolites. Notable differential pathways include starch and sucrose metabolism, amino acid sugar metabolism, and nucleotide sugar metabolism. The SWEET gene family was identified and analyzed, leading to the cloning of PpSWEET15 and subcellular localization. Overexpression of PpSWEET15 resulted in a significant decrease in sucrose content in leaves from 134.44 μg·g−1 to <10 μg·g−1. Glucose content decreased from 407.75 μg·g−1 to 318.38 μg·g−1, while fructose levels showed no significant difference between the two groups of leaves. This comprehensive transcriptomic and proteomic analysis provides valuable insights into the molecular mechanisms underlying the efficient accumulation of pectin in P. puberula.

Environmental concentrations of antibiotics induced polymyxin B tolerance in Aeromonas hydrophila.

Polymyxin B is one of the last lines of defense in infections caused by multidrug-resistant Gram-negative bacteria. Aeromonas hydrophila are important fish pathogens and the occurrence of polymyxin B-resistant A. hydrophila isolates is increasing. While investigating 14 environmental chemical pollutants that may affect bacterial polymyxin B sensitivity in aquatic bacteria, we discovered that tolerance of A. hydrophila to polymyxin B is increased by short-term (90min) concurrent exposure to tetracyclines, tigecycline or gentamicin at environmentally relevant concentrations (0.0625μg/mL) and persists as long as the inducer is present. The exposure increased the growth of A. hydrophila at an inhibitory concentration of polymyxin B. The increased polymyxin B tolerance was attributed to changes in gene expression, without alterations in genotype and independent of cell surface charge variations. Such changes are relate to six KEGG pathways, including ribosome, nucleotide metabolism, pyrimidine metabolism, glyoxylate and dicarboxylate metabolism, purine metabolism, starch and sucrose metabolism. The dysregulated genes were involved in broad physiological changes, such as cell motility, flagella biosynthesis, quorum sensing, biofilm formation, and chemotaxis. Furthermore, the up-regulation of genes encoding Mg2+ transport, biotin synthesis, lipoprotein, glycerol phospholipid metabolism, phospholipid transport, and the down-regulation of genes, such as ompK, yidD and ompA related to enhanced cell membrane barrier, may contribute to the increased polymyxin B tolerance in A. hydrophila. In summary, the study results revealed the impact of environmental antibiotics in promoting microbial polymyxin B tolerance. Our findings underscore the role of environmental antibiotics in promoting polymyxin B tolerance and provide insights into the mechanisms of polymyxin B tolerance evolution in A. hydrophila.

Whole Genome Identification and Integrated Analysis of Long Non-Coding RNAs Responding ABA-Mediated Drought Stress in Panax ginseng C.A. Meyer.

Panax ginseng C.A. Meyer is a perennial herb that is used worldwide for a number of medical purposes. Long non-coding RNAs (lncRNAs) play a crucial role in diverse biological processes but still remain poorly understood in ginseng, which has limited the application of molecular breeding in this plant. In this study, we identified 17,478 lncRNAs and 3106 novel mRNAs from ginseng by high-throughput illumine sequencing. 50 and 257 differentially expressed genes (DEGs) and DE lncRNAs (DELs) were detected under drought + ABA vs. drought conditions, respectively. The DEGs and DELs target genes main enrichment is focused on the "biosynthesis of secondary metabolites", "starch and sucrose metabolism", and "carbon metabolism" pathways under drought + ABA vs. drought conditions according to KEGG pathway enrichment analysis, suggesting that these secondary metabolites biosynthesis pathways might be crucial for ABA-mediated drought stress response in ginseng. Together, we identified drought stress response lncRNAs in ginseng for the first time and found that the target genes of these lncRNAs mainly regulate the biosynthesis of secondary metabolites pathway to response to drought stress. These findings also open up a new visual for molecular breeding in ginseng.