Lignin Involvement in Programmed Changes in Peach-Fruit Texture Indicated by Metabolite and Transcriptome Analyses

Decoding xenia effects on 'Jinsha' pomelo: Insights from physiological, transcriptomics and metabolomics analyses

'Xenia' is the terminology and biology of direct, or immediate, pollen effects on seeds and fruits. In this study, we found that the pollination of 'Jinsha' pomelo (JS) with pollen from Grapefruit (GR) and 'Majia' pomelo (MJ) led to significant differences in the seed numbers and primary metabolite (soluble sugar and amino acid). In pollinated pistils, the differences in the number of pollen tubes entering the embryo sac and the content of cytokinin components at 5 d post-pollination between the two pollen sources might be the important factor contributing to the discrepancies of seed trait and further affected fruit quality. In addition, joint analysis result of metabolomics and transcriptomics showed that the down-regulated expression of genes in the sucrose and starch metabolism pathways, glycolysis pathway and amino acid metabolism pathway of JS × MJ fruit compared to those of JS × GR fruit might also be resulted in an increase in the content of fructose and glucose and a decrease in the content of a large number of free amino acid components. This study revealed the reasons for the changes in seed and fruit characteristics induced by the xenia effect under two different pollen sources, and the hub genes novel.155 (HK), Cg2g040280 (bglX), Cg4g020710 (ISA), and Cg3g021210 (P4HA) were obtained by co-expression network analysis.

Multi-omics analyses reveal mechanism for high resistant starch formation in an indica rice SSIIIa mutant

Soluble starch synthase IIIa (SSIIIa) is a key enzyme involved in amylopectin biosynthesis in rice, and deficiency of SSIIIa results in high content of resistant starch, which is benefit to human health. However, little is known about metabolic differences and carbon re-allocation in the seeds of the indica rice ss3a mutant. We found that SSIIIa deficiency impaired the storage of starch, but increased the soluble sugars, free amino acids and lipids. By multi-omic analyses, we found inactivation of SSIIIa triggered carbon repartitioning by downregulating sucrose synthase, grain incomplete filling 1, fructokinase and hexokinase (HK), and promoted the accumulation of soluble sugars. Meanwhile, the downregulation of HK and upregulation of plastidic phosphoglucomutase reduced the carbon flow through glycolysis and promoted glycogenesis. The downregulation of OsbZIP58 and the deleterious effect on ribosome formation might result in the reduction of storage protein synthesis and increased free amino acids content in ss3a. The higher levels of amylose and lipids could form more amylose-lipid complexes (starch phospholipids), resulting in a higher resistant starch content. Taken together, our study unraveled a functional cross talk between starch, protein and lipids in rice endosperm during seed development of ss3a, providing new insights for formation of high resistant starch in rice.

Rhizosphere Mortierella strain of alfalfa exerted weed growth inhibition by inducing expression of plant hormone-related genes

Introduction

Weeds are significant factors that detrimentally affect crop health and hinder optimal herbage yield. Rhizosphere microorganisms play crucial roles in plant growth, development, and nutrient uptake. Therefore, research focusing on weed control through the lens of microorganisms has emerged as a prominent area of study. The oil-producing fungus Mortierella, which is known for its numerous agricultural benefits, has garnered significant attention in recent years.

Methods

In this study, we conducted inoculation experiments in a controlled artificial culture climate chamber to investigate the effects of differential hormones and differentially expressed genes in the stems and leaves of Digitaria sanguinalis using Liquid Chromatography Tandem Mass Spectrometry and RNA-seq techniques, respectively. Additionally, Pearson's correlation analysis was used to establish correlations between differential hormones and growth indicators of Digitaria sanguinalis.

Results and discussion

The results demonstrated that inoculation with Mortierella sp. MXBP304 effectively suppressed aboveground biomass and plant height in Digitaria sanguinalis. Furthermore, there was significant upregulation and downregulation in the expression of genes involved in the synthesis and metabolism of phenylalanine and L-phenylalanine. Conversely, the expression of genes related to tryptophan, L-tryptophan, and indole was significantly downregulated. The addition of Mortierella sp. MXBP304 can influence the gene expression associated with phenylalanine and tryptophan synthesis and metabolism during Digitaria sanguinalis growth, subsequently reducing the relative contents of phenylalanine and tryptophan, thereby directly inhibiting Digitaria sanguinalis growth.

Tea-Derived Polyphenols Enhance Drought Resistance of Tea Plants (Camellia sinensis) by Alleviating Jasmonate-Isoleucine Pathway and Flavonoid Metabolism Flow

Extreme drought weather has occurred frequently in recent years, resulting in serious yield loss in tea plantations. The study of drought in tea plantations is becoming more and more intensive, but there are fewer studies on drought-resistant measures applied in actual production. Therefore, in this study, we investigated the effect of exogenous tea polyphenols on the drought resistance of tea plant by pouring 100 mg·L-1 of exogenous tea polyphenols into the root under drought. The exogenous tea polyphenols were able to promote the closure of stomata and reduce water loss from leaves under drought stress. Drought-induced malondialdehyde (MDA) accumulation in tea leaves and roots was also significantly reduced by exogenous tea polyphenols. Combined transcriptomic and metabolomic analyses showed that exogenous tea polyphenols regulated the abnormal responses of photosynthetic and energy metabolism in leaves under drought conditions and alleviated sphingolipid metabolism, arginine metabolism, and glutathione metabolism in the root system, which enhanced the drought resistance of tea seedlings. Exogenous tea polyphenols induced jasmonic acid-isoleucine (JA-ILE) accumulation in the root system, and the jasmonic acid-isoleucine synthetase gene (TEA028623), jasmonic acid ZIM structural domain proteins (JAMs) synthesis genes (novel.22237, TEA001821), and the transcription factor MYC2 (TEA014288, TEA005840) were significantly up-regulated. Meanwhile, the flavonoid metabolic flow was significantly altered in the root; for example, the content of EGCG, ECG, and EGC was significantly increased. Thus, exogenous tea polyphenols enhance the drought resistance of tea plants through multiple pathways.

Metabolome and Transcriptome Analysis Revealed the Basis of the Difference in Antioxidant Capacity in Different Tissues of Citrus reticulata 'Ponkan'

Citrus is an important type of fruit, with antioxidant bioactivity. However, the variations in the antioxidant ability of different tissues in citrus and its metabolic and molecular basis remain unclear. Here, we assessed the antioxidant capacities of 12 tissues from Citrus reticulata 'Ponkan', finding that young leaves and root exhibited the strongest antioxidant capacity. Secondary metabolites accumulated differentially in parts of the citrus plant, of which flavonoids were enriched in stem, leaf, and flavedo; phenolic acids were enriched in the albedo, while coumarins were enriched in the root, potentially explaining the higher antioxidant capacities of these tissues. The spatially specific accumulation of metabolites was related to the expression levels of biosynthesis-related genes such as chalcone synthase (CHS), chalcone isomerase (CHI), flavone synthase (FNS), O-methyltransferase (OMT), flavonoid-3'-hydroxylase (F3'H), flavonoid-6/8-hydroxylase (F6/8H), p-coumaroyl CoA 2'-hydroxylase (C2'H), and prenyltransferase (PT), among others, in the phenylpropane pathway. Weighted gene co-expression network analysis (WGCNA) identified modules associated with flavonoids and coumarin content, among which we identified an OMT involved in coumarin O-methylation, and related transcription factors were predicted. Our study identifies key genes and metabolites influencing the antioxidant capacity of citrus, which could contribute to the enhanced understanding and utilization of bioactive citrus components.

Transcriptome analysis reveals genes related to the synthesis and metabolism of cell wall polysaccharides in goji berry (Lycium barbarum L.) from various regions

BACKGROUND

In goji berries (Lycium barbarum L.), the cell wall properties and ripening environment affect fruit quality and their economic benefits. However, the mechanism underlying the cell wall remains to be fully elucidated.

RESULTS

The results showed that total sugar content was higher in Qinghai berries (13.87%, P < 0.01), whereas cellulose content peaked in Zhongning berries (28%, P < 0.05). Arabinose, galactose, and galacturonic acid were the principal components of the cell wall polysaccharides in goji berries. Among them, the content of galactose in Zhongning was significantly the highest (P < 0.05). Interestingly, we found that highly expressed β-glucosidase and lowly expressed endoglucanase led to cellulose accumulation by RNA-sequencing analysis. The expression analysis results suggested that pectate lyase and pectinesterase enzymes could be major factors related to higher galactose and galacturonic acid contents in Zhongning compared to in Qinghai and Gansu. The starch and sucrose metabolism pathway, pentose and glucuronate interconversions pathway, and galactose metabolism pathway played a significant role in cell wall polysaccharide synthesis and metabolism.

CONCLUSION

In the present study, we aimed to provide some insights into the cell wall on polysaccharide composition, structural features, and gene analysis in goji berries from Zhongning, Qinghai, and Gansu in China. These results might help to clarify the molecular function of the major genes in the cell wall polysaccharides of goji berries and provide a solid foundation for further study. © 2023 Society of Chemical Industry.

Low temperature inhibits pectin degradation by PpCBFs to prolong peach storage time

Low-temperature storage is a widely used method for peach fruit storage. However, the impact of PpCBFs on pectin degradation during low-temperature storage is unclear. As such, in this study, we stored the melting-flesh peach cultivar "Fuli" at low temperature (LT, 6°C) and room temperature (RT, 25°C) to determine the effect of different temperatures on its physiological and biochemical changes. Low-temperature storage can inhibit the softening of "Fuli" peaches by maintaining the stability of the cell wall. It was found that the contents of water-soluble pectin and ionic-soluble pectin in peach fruit stored at RT were higher than those stored at LT. The enzyme activities of polygalacturonase (PG), pectate lyase (PL), and pectin methylesterase (PME) were all inhibited by LT. The expressions of PpPME3, PpPL2, and PpPG were closely related to fruit firmness, but PpCBF2 and PpCBF3 showed higher expression levels at LT than RT. The promoters of PpPL2 and PpPG contain the DER motif, which suggested that PpCBF2 and PpCBF3 might negatively regulate their expression by directly binding to their promoters. These results indicated that LT may maintain firmness by activating PpCBFs to repress pectin-degradation-related enzyme genes during storage.

Integrative analysis of the effects of organic and conventional farming methods on peanut based on transcriptome and metabolomics

To elucidate the nutritional quality of peanut under different farming methods, we selected two cultivars, "jihua13" and "jihua4", to grow in organic and conventional environments, respectively. After harvest, we measured physiological parameters and differential metabolites. Metabolomics showed that most of the amino acids, carbohydrates, and secondary metabolites in organically grown jihua4 were downregulated, which was completely the opposite in jihua13. Fatty acids associated with heart disease and hypertension are reduced in organically grown peanuts. In particular, the highly statistically significant tryptophan betaine seems to be used as a reference to distinguish between organic and conventional cultivation. Mechanisms leading to differences in crop chemical composition are explained by transcriptome analysis. The results of the transcriptome analysis indicated that organic cultivation largely affects the synthesis of amino acids and carbohydrates in jihua13. Combined analysis of transcriptome and metabolomics found that variety jihua13 is more sensitive to farming methods and produces more unsaturated fatty acids than jihua4.

Mitigation of Acetamiprid Residue Disruption on Pea Seed Germination by Selenium Nanoparticles and Lentinans

The use of pesticides for pest control during the storage period of legume seeds is a common practice. This study evaluated the disruptive effects on pea seed germination and the repair effects of selenium nanoparticles (SeNPs) and lentinans (LNTs) This study examined the biomass, nutrient content, antioxidant indicators, plant hormones, phenolic compounds, and metabolites associated with the lignin biosynthesis pathway in pea sprouts. The application of acetamiprid resulted in a significant decrease in yield, amino-acid content, and phenolic compound content of pea sprouts, along with observed lignin deposition. Moreover, acetamiprid residue exerted a notable level of stress on pea sprouts, as evidenced by changes in antioxidant indicators and plant hormones. During pea seed germination, separate applications of 5 mg/L SeNPs or 20 mg/L LNTs partially alleviated the negative effects induced by acetamiprid. When used in combination, these treatments restored most of the aforementioned indicators to levels comparable to the control group. Correlation analysis suggested that the regulation of lignin content in pea sprouts may involve lignin monomer levels, reactive oxygen species (ROS) metabolism, and plant hormone signaling mediation. This study provides insight into the adverse impact of acetamiprid residues on pea sprout quality and highlights the reparative mechanism of SeNPs and LNTs, offering a quality assurance method for microgreens, particularly pea sprouts. Future studies can validate the findings of this study from the perspective of gene expression.

Lignin Biosynthesis in Postharvest Water Bamboo (Zizania latifolia) Shoots during Cold Storage Is Regulated by RBOH-Mediated Reactive Oxygen Species Signaling

Lignification is a major cause of senescence in fresh shoots of water bamboo (Zizania latifolia), which is a popular vegetable in southeast Asia; however, its physiological and molecular mechanisms is less understood. In the present study, lignin content and transcriptome change in postharvested water bamboo shoots under cold storage were investigated. We found that lignin significantly accumulated in the epidermis of the shoots with the increase of firmness. In the cold storage shoots, the major up-regulated genes were involved in phenylpropanoid biosynthesis, plant-pathogen interactions, and starch and sucrose metabolism. The lignin biosynthesis genes PAL, 4CL, C4H, CCoAOMT, CCR, F5H, CAD, and POD family were up-regulated during cold storage, while HCT and C3H were down-regulated. The MAPK signaling pathway was also up-regulated and respiratory burst oxidase homologue (RBOH) genes were strongly up-regulated. Therefore, we investigated the RBOH gene family and their expression profile in water bamboo shoots. The results indicated that 10 ZlRBOHs were up-regulated in cold storage shoots. Diphenyleneiodonium chloride (DPI), an inhibitor of RBOH oxidase, significantly inhibited the expression of genes involved in lignin deposition and biosynthesis, while H2O2 enhanced these processes. These results suggest that lignification of water bamboo shoots is regulated by RBOH-mediated ROS signaling.

EuRBG10 involved in indole alkaloids biosynthesis in Eucommia ulmoides induced by drought and salt stresses

Alkaloids are natural products with many important medicinal activities. To explore the mechanism of abiotic stress promoting alkaloid biosynthesis in Eucommia ulmoides, transcriptomic analysis and metabonomic analysis were used, virus-induced gene silencing (VIGS) lines of target gene were constructed. The results showed that drought and salt stress caused wilting and blackening of leaves, decreased chlorophyll level, and significantly induced MDA and relative conductivity. To resist the damage of stress to cells, the level of secondary metabolites such as alkaloids increased significantly with the extension of stress time. Transcriptomic results showed that, were. Six alkaloid related genes (AWGs) were gathered in five modules positively correlated with either salt stress or alkaloid contents by WGCNA. Results of GO and KEGG enrichment revealed that biosynthesis of alkaloid, especially indole alkaloid was induced, and degradation of alkaloid was inhibited under salt stress. Combining the results of transcriptome and metabolomics, it was suggested that EuRBG10 promotes the production of indole alkaloids and EuAMO5 inhibits the degradation of alkaloids, which may be the core mechanism of the indole alkaloid biosynthesis pathway (map00901) induced by salt stress. The results of these hub proteins were also consistent with the chordal graph of KEGG enrichment. Hub roles of EuRGB10 was checked in E. ulmoides by VIGS. Our findings provide a preliminary understanding of abiotic stress regulating secondary metabolites such as alkaloids, and propose hub genes that can be used to improve the level of bioactive components in medicinal plant.

Combined Proteomic and Metabolomic Analysis of the Molecular Mechanism Underlying the Response to Salt Stress during Seed Germination in Barley

Salt stress is a major abiotic stress factor affecting crop production, and understanding of the response mechanisms of seed germination to salt stress can help to improve crop tolerance and yield. The differences in regulatory pathways during germination in different salt-tolerant barley seeds are not clear. Therefore, this study investigated the responses of different salt-tolerant barley seeds during germination to salt stress at the proteomic and metabolic levels. To do so, the proteomics and metabolomics of two barley seeds with different salt tolerances were comprehensively examined. Through comparative proteomic analysis, 778 differentially expressed proteins were identified, of which 335 were upregulated and 443 were downregulated. These proteins, were mainly involved in signal transduction, propanoate metabolism, phenylpropanoid biosynthesis, plant hormones and cell wall stress. In addition, a total of 187 salt-regulated metabolites were identified in this research, which were mainly related to ABC transporters, amino acid metabolism, carbohydrate metabolism and lipid metabolism; 72 were increased and 112 were decreased. Compared with salt-sensitive materials, salt-tolerant materials responded more positively to salt stress at the protein and metabolic levels. Taken together, these results suggest that salt-tolerant germplasm may enhance resilience by repairing intracellular structures, promoting lipid metabolism and increasing osmotic metabolites. These data not only provide new ideas for how seeds respond to salt stress but also provide new directions for studying the molecular mechanisms and the metabolic homeostasis of seeds in the early stages of germination under abiotic stresses.

Integrative analysis of the metabolome and transcriptome reveals the molecular mechanism of chlorogenic acid synthesis in peach fruit

As the most abundant phenolic acid in peach fruit, chlorogenic acid (CGA) is an important entry point for the development of natural dietary supplements and functional foods. However, the metabolic and regulation mechanisms underlying its accumulation in peach fruits remain unclear. In this study, we evaluated the composition and content of CGAs in mature fruits of 205 peach cultivars. In peach fruits, three forms of CGA (52.57%), neochlorogenic acid (NCGA, 47.13%), and cryptochlorogenic acid (CCGA, 0.30%) were identified. During the growth and development of peach fruits, the content of CGAs generally showed a trend of rising first and then decreasing. Notably, the contents of quinic acid, shikimic acid, p-coumaroyl quinic acid, and caffeoyl shikimic acid all showed similar dynamic patterns to that of CGA, which might provide the precursor material basis for the accumulation of CGA in the later stage. Moreover, CGA, lignin, and anthocyanins might have a certain correlation and these compounds work together to maintain a dynamic balance. By the comparative transcriptome analysis, 8 structural genes (Pp4CL, PpCYP98A, and PpHCT) and 15 regulatory genes (PpMYB, PpWRKY, PpERF, PpbHLH, and PpWD40) were initially screened as candidate genes of CGA biosynthesis. Our findings preliminarily analyzed the metabolic and molecular regulation mechanisms of CGA biosynthesis in peach fruit, which provided a theoretical basis for developing high-CGA content peaches in future breeding programs.

Combined Transcriptome and Metabolome Analyses Reveal Candidate Genes Involved in Tangor (Citrus reticulata × Citrus sinensis) Fruit Development and Quality Formation

Tangor, an important citrus type, is a hybrid of orange and mandarin and possesses their advantageous characteristics. Fruit quality is an important factor limiting the development of the citrus industry and highly depends on fruit development and ripening programs. However, fruit development and quality formation have not been completely explored in mandarin-orange hybrids. We sequenced the metabolome and transcriptome of three mandarin-orange hybrid cultivars at the early fruiting [90 days after full bloom (DAFB)], color change (180 DAFB), and ripening (270 DAFB) stages. Metabolome sequencing was performed to preliminarily identify the accumulation patterns of primary and secondary metabolites related to fruit quality and hormones regulating fruit development. Transcriptome analysis showed that many genes related to primary metabolism, secondary metabolism, cell wall metabolism, phytohormones, and transcriptional regulation were up-regulated in all three cultivars during fruit development and ripening. Additionally, multiple key genes were identified that may play a role in sucrose, citric acid and flavonoid accumulation, cell wall modification, and abscisic acid signaling, which may provide a valuable resource for future research on enhancement of fruit quality of hybrid citrus. Overall, this study provides new insights into the molecular basis of pulp growth and development regulation and fruit quality formation in mandarin-orange hybrids.

Metabolomic and transcriptomic investigation of the mechanism involved in enantioselective toxicity of imazamox in Lemna minor

Imazamox (IM) is a chiral pesticide that has been widely used in agriculture. Currently, few studies have investigated the toxicity mechanisms of imazamox to aquatic macrophyte from the enantiomer level. In this study, the enantioselective effects of IM on the toxicity and physiological and biochemical system of aquatic macrophyte Lemna minor were systematically investigated. Metabolomic and transcriptomic for Lemna minor were used to identify potential mechanisms of toxicity. 7 d EC₅₀s for racemic-, R-, and S-IM were 0.036, 0.035, and 0.203 mg/L, respectively, showing enantioselective toxicity. In addition, IM caused Lemna minor lipid peroxidation and antioxidant damage, and inhibited the activities of the target enzymes. Metabolomic and transcriptomic data indicated that R-IM interferenced differentially expressed genes and metabolites of Lemna minor which were enriched in carbon fixation during photosynthesis, glutathione metabolic pathway, pentose phosphate pathway, zeatin biosynthesis, and porphyrin and chlorophyll metabolism. S-IM affected phenylalanine metabolism, phenylpropanoid biosynthesis, zeatin biosynthesis and secondary metabolite biosynthesis. Racemic-IM influenced carbon fixation during operation, glutathione metabolic pathway, zeatin biosynthesis and pentose phosphate pathway. The results provide new insights into the enantioselective toxicity mechanisms of IM to Lemna minor, and lay the foundation for conducting environmental risk assessments.

Analyses of key gene networks controlling carotenoid metabolism in Xiangfen 1 banana

BACKGROUND

Banana fruits are rich in various high-value metabolites and play a key role in the human diet. Of these components, carotenoids have attracted considerable attention due to their physiological role and human health care functions. However, the accumulation patterns of carotenoids and genome-wide analysis of gene expression during banana fruit development have not been comprehensively evaluated.

RESULTS

In the present study, an integrative analysis of metabolites and transcriptome profiles in banana fruit with three different development stages was performed. A total of 11 carotenoid compounds were identified, and most of these compounds showed markedly higher abundances in mature green and/or mature fruit than in young fruit. Results were linked to the high expression of carotenoid synthesis and regulatory genes in the middle and late stages of fruit development. Co-expression network analysis revealed that 79 differentially expressed transcription factor genes may be responsible for the regulation of LCYB (lycopene β-cyclase), a key enzyme catalyzing the biosynthesis of α- and β-carotene.

CONCLUSIONS

Collectively, the study provided new insights into the understanding of dynamic changes in carotenoid content and gene expression level during banana fruit development.

Integrated Metabolomics and Transcriptome Analyses Unveil Pathways Involved in Sugar Content and Rind Color of Two Sugarcane Varieties

Metabolic composition can have potential impact on several vital agronomic traits, and metabolomics, which represents the bioactive compounds in plant tissues, is widely considered as a powerful approach for linking phenotype-genotype interactions. However, metabolites related to cane traits such as sugar content, rind color, and texture differences in different sugarcane cultivars using metabolome integrated with transcriptome remain largely inconclusive. In this study, metabolome integrated with transcriptome analyses were performed to identify and quantify metabolites composition, and have better insight into the molecular mechanisms underpinning the different cane traits, namely, brix, rind color, and textures in the stems (S) and leaves (L) of sugarcane varieties FN41 and 165402. We also identified metabolites and associated genes in the phenylpropanoid and flavonoid biosynthesis pathways, starch and sucrose metabolism. A total of 512 metabolites from 11 classes, with the vast majority (122) belonging to flavonoids were identified. Moreover, the relatively high amount of D-fructose 6-p, D-glucose6-p and glucose1-p detected in FN41L may have been transported and distributed by source and sink of the cane, and a majority of them reached the stem of sugarcane FN41L, thereby promoting the high accumulation of sugar in FN41S. Observations also revealed that genes such as C4H, CHS, F3H, F3'H, DFR, and FG2 in phenylpropanoid and flavonoid biosynthesis pathways were the major factors impacting the rind color and contrasting texture of FN41 and 165204. Further analysis revealed that weighted gene co-expression network analysis (WGCNA) hub genes and six transcription factors, namely, Tify and NAC, MYB-related, C2C2-Dof, WRKY, and bHLH play a key role in phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, starch and sucrose metabolism. Additionally, metabolites such as L-phenylalanine, tyrosine, sinapaldehyde, pinobanksin, kaempferin, and nictoflorin were the potential drivers of phenotypic differences. Our finding also demonstrated that genes and metabolites in the starch and sucrose metabolism had a significant effect on cane sugar content. Overall, this study provided valuable insight into the molecular mechanisms underpinning high sugar accumulation and rind color in sugarcane, which we believe is important for future sugarcane breeding programs and the selection of high biomass varieties.

Integrative analyses of metabolome and transcriptome reveals metabolomic variations and candidate genes involved in sweet cherry (Prunus avium L.) fruit quality during development and ripening

Sweet cherry (Prunus avium L.), one of the most appreciated and most important commercial temperate fruits, has high sensory quality and nutritional value. Investigating its metabolic variations provides valuable information on the formation of fruit quality. In this study, widely targeted LC-MS/MS based metabolomics was used to identify and quantify metabolic changes during 'Black Pearl' sweet cherry development and ripening. A total of 263 significant differentially expressed metabolites (DEMs) were detected during the four fruit-development stages. Significant differences were observed in the composition and content of compounds in the four stages of cherry development, especially sugars, organic acids, and flavonoids. Moreover, transcriptome analysis provided a molecular basis for metabolic variations during fruit development. A total of 6724 significant differentially expressed genes (DEGs) were identified. Further correlation analysis of major DEMs and DEGs showed that 19 key DEGs were involved in sugar metabolism, 23 key DEGs in organic acid metabolism, and 13 key DEGs in flavonoid metabolism. The upregulated genes involved in the flavonoid pathway probably play an important role in regulating the rapid increase of anthocyanin content during fruit development. These comprehensive analysis data provide a better understanding to improve fruit quality traits based on molecular and metabolic levels.

Genomic and transcriptomic analyses of Citrus sinensis varieties provide insights into Valencia orange fruit mastication trait formation

Valencia orange (Citrus sinensis Osbeck) (VO) is a type of late-ripening sweet orange whose ripening occurs 4 to 5 months later than that of the mid-ripening common sweet orange (CO). Notably, the mastication trait of VO fruit is inferior to that of CO fruit. To date, how inferior pulp mastication trait forms in VO has not been determined. In this study, 13 VO varieties and 12 CO varieties were subjected to whole-genome resequencing. A total of 2.98 million SNPs were identified from 25 varieties, and a SNP molecular marker was developed to distinguish VO and CO. Moreover, 144 and 141 genes identified by selective sweep analysis were selected during VO and CO evolution, respectively. Based on gene functional enrichment analysis, most of the selected VO genes were related to the stress response and lignin biosynthesis. Simultaneously, we comparatively analyzed the transcriptome profiles of peel and pulp tissues among three VO varieties and three CO varieties, and the results demonstrated differences in lignin biosynthesis between VO and CO fruits. Furthermore, coexpression network analysis was performed to identify hub genes of lignin-related and variety-specific networks, which included CsERF74, CsNAC25, CsHSFB3, CsSPL4/13, etc. Overall, this study provides important insights into the mastication trait formation of Valencia orange fruit.

Omics analyses indicate the routes of lignin related metabolites regulated by trypsin during storage of pitaya (Hylocereus undatus)

The storage quality of Hylocereus undatus was significantly improved by trypsin, a novel preservative. The transcriptomic results revealed that antioxidant signal pathways were induced, while lignin catabolic process was impeded by trypsin. In addition, the results of protein-protein interaction (PPI) network networks suggested that flavone 3'-O-methyltransferase 1 (OMT1), ferulic acid 5-hydroxylase 1 (CYP84A1), cellulose synthase isomer (CEV1), and 4-coumarate-CoA ligase 3 (4CL3) act as hubs of peroxidases, lignin related proteins, and proteins involved in the phenylpropanoid metabolism (PLPs) induced by trypsin. Trypsin also regulated the biosynthesis of lignin, chlorogenic acid, and flavonoids. Caffeic acid might be the hub in the metabolic network of the early pathways of phenylpropanoid biosynthesis. It has been hypothesized that trypsin might quickly induce lignin biosynthesis and then up-regulated bioactive metabolites to enhance storage quality of H. undatus.

CsHCT-Mediated Lignin Synthesis Pathway Involved in the Response of Tea Plants to Biotic and Abiotic Stresses

Many studies have shown that phenolic compounds such as lignin and flavonoids enhance plant resistance. Tea plants are rich in flavonoid compounds. Whether these compounds are related to tea plant resistance is unclear. In this study, an interesting conclusion was drawn on the basis of experimental results: in response to abiotic stress (except for sucrose treatment), gene expression was increased in the phenylpropanoid and lignin pathways and was reduced in the flavonoid pathway in tea plants. CsHCTs, the genes located at the branch point of the lignin and flavonoid pathways, are most suitable for regulating the ratio of carbon flow in the lignin pathway and flavonoid synthesis. Enzymatic and genetic modification experiments proved that CsHCTs encode hydroxycinnamoyl-coenzyme A:shikimate/quinate hydroxycinnamoyl transferase in vitro and in vivo. Furthermore, the genetic modification results showed that the contents of phenolic acids and lignin were increased in tobacco and Arabidopsis plants overexpressing CsHCTs, whereas the content of flavonol glycosides was decreased. Both types of transgenic plants showed resistance to many abiotic stresses and bacterial infections. We speculate that CsHCTs participate in regulation of the metabolic flow of carbon from the flavonoid pathway to the chlorogenic acid, caffeoylshikimic acid, and lignin pathways to increase resistance to biotic and abiotic stresses.

Plant metabolomics integrated with transcriptomics and rhizospheric bacterial community indicates the mitigation effects of Klebsiella oxytoca P620 on p-hydroxybenzoic acid stress in cucumber

Accumulation of p-hydroxybenzoic acid (PHBA) in soil causes autotoxicity stress in cucumber. When the stress is mitigated by PHBA-degrading bacteria, plant metabolites have not been detected. To explore mechanisms underlining the mitigation, plant metabolites have not been combined with rhizospheric microbes, antioxidant and soil enzymes. In this study, a strain P620 of Klebsiella decomposed PHBA to acetyl CoA. Cucumber was sown into soil supplemented with P620 and/or PHBA. After addition with P620, P620 colonization and the enriched bacterial genera were observed in rhizosphere. Compared to PHBA stress alone, the combination of P620 application and PHBA stress improved plant growth, decreased PHBA concentration in soil, and increased the activities of five soil enzymes and eight antioxidant enzymes in leaves. Metabolomic and transcriptomic analysis highlighted that P620 application decreased the intensities of MAG(18:3) isomer 4, MAG(18:3) isomer 2, lysoPC 18:3 (2n isomer), 2'-deoxyadenosine-5'-monophosphate, pyridoxine, and glucarate O-phosphoric acid in PHBA-stressed leaves and down-regulated the expression of genes related to these metabolites. We propose a mechanism that P620 application alters microbial communities in PHBA-contaminated soil. Thus, the application reduces PHBA concentration in soil, activates antioxidant and soil enzymes, and also influences metabolites in leaves by affecting plant transcriptome, mitigating PHBA stress in cucumber.

Novel Insight into the Relationship between Metabolic Profile and Fatty Acid Accumulation Altering Cellular Lipid Content in Pineapple Fruits at Different Stages of Maturity

Pineapple fruits are usually harvested at different stages of maturity, based on consumer demands. The stage of maturity significantly affects the storage tolerance due to alterations in the cellular lipid homeostasis in the fruits. The characteristic abundance of metabolites and fatty acids (FAs) can provide vital information giving insight into the cellular lipid changes that occur during the ripening process in the fruits. Here, liquid chromatography-tandem mass spectrometry, largely based on the analysis of widely targeted metabolomics, was applied to evaluate the differences in the metabolites among the pineapple at three different stages of maturity namely, pineapples at the young fruit (YF), mature fruit (MF), and fully mature fruit (FMF) stages. In this study, 466 metabolites were annotated and identified. Among these, 59 lipids, including the glyceride esters, fatty acids and conjugates, and lysophospholipids (LPLs) were characterized. Notably, the LPLs were down-regulated in their relative abundance in the MF compared with the YF, and subsequently they remained almost stable in the FMF stage. The FA profiling results revealed the presence of certain unsaturated fatty acids (UFAs); besides, the total monounsaturated fatty acid (MUFA) to saturated fatty acid (SFA) ratio, as well as the polyunsaturated fatty acids (PUFA) to SFA ratio, showed noticeable decrease during the ripening process. The differential accumulation patterns of the LPLs, MUFAs, PUFAs, and SFAs imply that the lipid degradation and peroxidation take place in the pineapple fruits from the YF to MF and YF to FMF stages, respectively. The present study provides new insights into the alterations in the cellular lipid metabolism underlying the metabolite profiles and accumulation of FAs in pineapple fruits during ripening.

Insulin-Mimic Components in Acer truncatum Leaves: Bio-Guided Isolation, Annual Variance Profiling and Regulating Pathway Investigated by Omics

Insulin mimic can promote transporting glucose to muscle tissue and accelerate glucose consumption. It is commonly occurring in many functional foods or traditional medicines. Anti-diabetes molecules from food sources are highly safe and suitable for long-term use to prevent early diabetes. The leaves of Acer truncatum was found glucose uptake promotion in our phenotypic screening. However, its bioactive components and mechanism are still unclear. We collected leaves from trees of different ages (2, 3, 4, 7 and 11 years old) and profiled the ingredients by LC-MS/MS. The essential active component (myricitrin) was acquired following bio-guide on a whole organism Zebrafish (Danio rerio). Its content in the leaves was not affected by tree ages. Therefore, myricitrin can serve as a quality mark for functional foods derived from A. truncatum leaves. The transcriptomic and metabolomic analysis in Zebrafish explored the differentially expressed genes and metabolites. Based on joint-pathway enrichment and qRT-PCR verification, the critical bioactive component myricitrin was found to affect toll-like receptors signaling pathways to regulate glucose uptake. Our findings disclosed a bioactive marker (myricitrin) in A. truncatum leaves and explored its regulation mechanism, which rationalized the anti-diabetes function of the herbal food.

Integrated Transcriptome and Metabolome Analysis Revealed That Flavonoid Biosynthesis May Dominate the Resistance of Zanthoxylum bungeanum against Stem Canker

Stem canker of Zanthoxylum bungeanum is a devastating disease that seriously affects the plantation and industrial development of Z. bungeanum due to a lack of effective control measures. The objective of this study was to screen out resistant Z. bungeanum varieties and further explore their resistance mechanisms against stem canker. Results showed that the most resistant and susceptible varieties were, respectively, Doujiao (DJ) and Fengxian Dahongpao (FD). Combining transcriptomic and metabolomic analyses, we found that the genes and metabolites associated with the phenylpropanoid metabolism, especially flavonoid biosynthesis, were highly significantly enriched in DJ following pathogen infection compared with that in FD, which indicated that the flavonoid metabolism may positively dominate the resistance of Z. bungeanum. This finding was further confirmed by quantitative real-time polymerase chain reaction analysis, through which higher expression levels of core genes involved in flavonoid metabolism in resistant variety were observed. Moreover, by analyzing the differences in the flavonoid content in the stems of resistant and susceptible varieties and the antifungal activities of flavonoids extracted from Z. bungeanum stems, the conclusion that flavonoid metabolism positively regulates the resistance of Z. bungeanum was further supported. Our results not only aid in better understanding the resistance mechanisms of Z. bungeanum against stem canker but also promote the breeding and utilization of resistant varieties.

Effects of Different Short-Term UV-B Radiation Intensities on Metabolic Characteristics of Porphyra haitanensis

The effects of ultraviolet (UV) radiation, particularly UV-B on algae, have become an important issue as human-caused depletion of the protecting ozone layer has been reported. In this study, the effects of different short-term UV-B radiation on the growth, physiology, and metabolism of Porphyra haitanensis were examined. The growth of P. haitanensis decreased, and the bleaching phenomenon occurred in the thalli. The contents of total amino acids, soluble sugar, total protein, and mycosporine-like amino acids (MAAs) increased under different UV-B radiation intensities. The metabolic profiles of P. haitanensis differed between the control and UV-B radiation-treated groups. Most of the differential metabolites in P. haitanensis were significantly upregulated under UV-B exposure. Short-term enhanced UV-B irradiation significantly affected amino acid metabolism, carbohydrate metabolism, glutathione metabolism, and phenylpropane biosynthesis. The contents of phenylalanine, tyrosine, threonine, and serine were increased, suggesting that amino acid metabolism can promote the synthesis of UV-absorbing substances (such as phenols and MAAs) by providing precursor substances. The contents of sucrose, D-glucose-6-phosphate, and beta-D-fructose-6-phosphate were increased, suggesting that carbohydrate metabolism contributes to maintain energy supply for metabolic activity in response to UV-B exposure. Meanwhile, dehydroascorbic acid (DHA) was also significantly upregulated, denoting effective activation of the antioxidant system. To some extent, these results provide metabolic insights into the adaptive response mechanism of P. haitanensis to short-term enhanced UV-B radiation.

Metabolomic and Transcriptomic Profiling Provide Novel Insights into Fruit Ripening and Ripening Disorder Caused by 1-MCP Treatments in Papaya

Treatment with 1-methylcyclopropylene (1-MCP) is an effective technique to preserve fruits, but inappropriate treatment with 1-MCP causes a ripening disorder (rubbery texture) in papaya fruit. In this study, a combined metabolomic and transcriptomic analysis was conducted to reveal the possible mechanism of the ripening disorder caused by unsuitable 1-MCP in papaya. A total of 203 differential accumulated metabolites (DAMs) were identified in the metabolome analysis. Only 24 DAMs were identified in the control (CK) vs. the 1-MCP 2 h group, and they were primarily flavonoids. Ninety and 89 DAMs were identified in the CK vs. 1-MCP 16 h and 1-MCP 2 h vs. 1-MCP 16 h groups, respectively, indicating that long-term 1-MCP treatment severely altered the metabolites during fruit ripening. 1-MCP 16 h treatment severely reduced the number of metabolites, which primarily consisted of flavonoids, lipids, phenolic acids, alkaloids, and organic acids. An integrated analysis of RNA-Seq and metabolomics showed that various energy metabolites for the tricarboxylic acid cycle were reduced by long-term treatment with 1-MCP, and the glycolic acid cycle was the most significantly affected, as well as the phenylpropane pathway. These results provide valuable information for fruit quality control and new insight into the ripening disorder caused by unsuitable treatment with 1-MCP in papaya.

Catechin gallate acts as a key metabolite induced by trypsin in Hylocereus undatus during storage indicated by omics

Trypsin is a novel superoxide scavenger. The storage quality of H. undatus was significantly improved by trypsin. To investigate the mechanism of flavonoid metabolism regulated by trypsin, combined analysis of widely targeted metabolomic and transcriptome were performed. GO and KEGG enrichment analyses of the transcriptome profiles of H. undatus revealed that some of the flavonoid related biosynthesis pathways were regulated by up or down patterns with the treatment of trypsin. Correlation analysis of flavonoid related genes expression in H. undatus provided a rationale for the functional significance of them. Furthermore, it has been revealed that the most significantly regulated flavonoid was catechin gallate in metabolomic profiles of H. undatus. The major route of flavonoid biosynthesis regulated by trypsin was also illustrated by both transcriptomic and metabolomic data. Finally, the results of PPI network revealed that C4H, HCT, and CYP75B1 acted as hub proteins involved in flavonoid metabolism regulated by trypsin.

Metabolomic and Transcriptomic Analyses of Anthocyanin Biosynthesis Mechanisms in the Color Mutant Ziziphus jujuba cv. Tailihong

The purplish-red color of "Tailihong" jujube fruit skins is caused primarily by anthocyanin accumulation, but the mechanisms that underlie anthocyanin biosynthesis in jujube fruit have rarely been studied. We performed metabolomic and transcriptomic analyses of jujube fruit skins at different developmental stages and identified a total of 158 flavonoids, among which cyanidin-3-O-rutinoside and peonidin-3,5-O-diglucoside were the primary anthocyanins. During fruit development and maturation, the anthocyanin content was strongly correlated with the expression of ZjANS and ZjUGT79B1, suggesting that these are key genes in the anthocyanin biosynthesis process. Transcriptomic analysis indicated that the transcription factors ZjMYB5, ZjTT8, and ZjWDR3 regulated anthocyanin biosynthesis in jujube fruit skins. Subcellular localization experiments confirmed that ZjANS and ZjUGT79B1 were localized to the nucleus and the endoplasmic reticulum. ZjMYB5 and ZjTT8 were found only in the nucleus, whereas strong fluorescence signals from ZjWDR3 were observed in the nucleus and cytoplasm. Prokaryotic expression and in vitro enzyme activity assays showed that the recombinant ZjANS protein catalyzed the formation of cyanidin from (+)-catechin. Secondary glycosylation by ZjUFGT79B1 modified cyanidin-3-O-glucoside to produce cyanidin-3-O-rutinoside, and ZjCCoAOMT readily catalyzed the production of the methylated anthocyanin peonidin-3,5-O-diglucoside from cyanidin 3,5-O-glucoside. Dual-Luciferase and GUS activity assays showed that the ZjANS and ZjUGT79B1 promoters were activated by ZjMYB5, ZjTT8, and ZjWDR3. All data indicated that these three transcription factors played important roles in anthocyanin biosynthesis in the color mutant Ziziphus jujuba cv. Tailihong, contributing to anthocyanin accumulation by enhancing the expression of ZjANS and ZjUGT79B1.

Multiomic Analysis Elucidates the Reasons Underlying the Differential Metabolite Accumulation in Citrus Mature Leaves and Fruit Juice Sacs

Fruit and leaf possess distinctly different metabolites. Here, metabolites and transcriptome were compared between mature leaves (ML) and juice sacs (JS) of Citrus grandis "Hirado Buntan" to investigate the possible reasons. Results indicated that the remarkable difference in starch, total flavonoids and carotenoids, l-ascorbate, and jasmonic acid between ML and JS was tightly related to the expression levels of their biosynthesis-related genes, while the significant difference in abscisic acid and citrate was mainly related to the gene expression level(s) of 9-cis-epoxycarotenoid dioxygenase and proton pump genes, respectively. In addition, ATP citrate lyase probably plays a key role in the levels of flavonoids between ML and JS via providing different levels of acetyl-CoA. Taken together, these results identified some key candidate genes responsible for the content of a given metabolite and will contribute to research in regulating such metabolite content in citrus fruits.

Transcriptome and metabolite profiling reveals the effects of Funneliformis mosseae on the roots of continuously cropped soybeans

BACKGROUND

Arbuscular mycorrhizal fungi are the most widely distributed mycorrhizal fungi, which can form mycorrhizal symbionts with plant roots and enhance plant stress resistance by regulating host metabolic activities. In this paper, the RNA sequencing and ultra-performance liquid chromatography (UPLC) coupled with tandem mass spectrometry (MS/MS) technologies were used to study the transcriptome and metabolite profiles of the roots of continuously cropped soybeans that were infected with F. mosseae and F. oxysporum. The objective was to explore the effects of F. mosseae treatment on soybean root rot infected with F. oxysporum.

RESULTS

According to the transcriptome profiles, 24,285 differentially expressed genes (DEGs) were identified, and the expression of genes encoding phenylalanine ammonia lyase (PAL), trans-cinnamate monooxygenase (CYP73A), cinnamyl-CoA reductase (CCR), chalcone isomerase (CHI) and coffee-coenzyme o-methyltransferase were upregulated after being infected with F. oxysporum; these changes were key to the induction of the soybean's defence response. The metabolite results showed that daidzein and 7,4-dihydroxy, 6-methoxy isoflavone (glycine), which are involved in the isoflavone metabolic pathway, were upregulated after the roots were inoculated with F. mosseae. In addition, a substantial alteration in the abundance of amino acids, phenolic and terpene metabolites all led to the synthesis of defence compounds. An integrated analysis of the metabolic and transcriptomic data revealed that substantial alterations in the abundance of most of the intermediate metabolites and enzymes changed substantially under pathogen infection. These changes included the isoflavonoid biosynthesis pathway, which suggests that isoflavonoid biosynthesis plays an important role in the soybean root response.

CONCLUSION

The results showed that F. mosseae could alleviate the root rot caused by continuous cropping. The increased activity of some disease-resistant genes and disease-resistant metabolites may partly account for the ability of the plants to resist diseases. This study provides new insights into the molecular mechanism by which AMF alleviates soybean root rot, which is important in agriculture.

Nutritional component changes in Xiangfen 1 banana at different developmental stages

Banana is an essential food resource in many tropical and subtropical countries. Metabolites in banana greatly influence its nutritional value and flavor. However, metabolic changes that occur in different developmental stages have not been comprehensively evaluated. In this study, widely targeted metabolomics based on multiple reaction monitoring was used in investigating dynamic changes in metabolites at three stages of fruit development. A total of 655 metabolites were identified in all the stages. A hierarchical cluster analysis of metabolites showed six clear expression patterns at the three developmental stages, and 69 up-regulated differential metabolites were identified in mature fruits compared with young and mature green fruits. A metabolic pathway analysis of differential metabolites showed significant enrichment of the flavonoid biosynthesis pathway and the phenylalanine, tyrosine, and tryptophan biosynthesis pathways. These results may serve as a reference for the isolation and identification of functional compounds from banana and for their sufficient utilization in the future.

Characterization of cold stress responses in different rapeseed ecotypes based on metabolomics and transcriptomics analyses

The winter oilseed ecotype is more tolerant to low temperature than the spring ecotype. Transcriptome and metabolome analyses of leaf samples of five spring Brassica napus L. (B. napus) ecotype lines and five winter B. napus ecotype lines treated at 4 °C and 28 °C were performed. A total of 25,460 differentially expressed genes (DEGs) of the spring oilseed ecotype and 28,512 DEGs of the winter oilseed ecotype were identified after cold stress; there were 41 differentially expressed metabolites (DEMs) in the spring and 47 in the winter oilseed ecotypes. Moreover, more than 46.2% DEGs were commonly detected in both ecotypes, and the extent of the changes were much more pronounced in the winter than spring ecotype. By contrast, only six DEMs were detected in both the spring and winter oilseed ecotypes. Eighty-one DEMs mainly belonged to primary metabolites, including amino acids, organic acids and sugars. The large number of specific genes and metabolites emphasizes the complex regulatory mechanisms involved in the cold stress response in oilseed rape. Furthermore, these data suggest that lipid, ABA, secondary metabolism, signal transduction and transcription factors may play distinct roles in the spring and winter ecotypes in response to cold stress. Differences in gene expression and metabolite levels after cold stress treatment may have contributed to the cold tolerance of the different oilseed ecotypes.

Hybrid Label-Free Molecular Microscopies for Simultaneous Visualization of Changes in Cell Wall Polysaccharides of Peach at Single- and Multiple-Cell Levels during Postharvest Storage

Softening of fruit during the postharvest storage, which is mainly associated with both compositional and spatial changes of polysaccharides within cell wall, affects the texture and quality of fruit. Current research on the fruit softening mechanism lacks an understanding of the overall softening at the cell level. The objective of this work was to investigate the change in the spatial distribution of cell wall polysaccharides in peach flesh cells at both single- and multiple-cell levels in a label-free way during the postharvest storage. Nonmelting peaches (Prunus persica L. Batsch cv."Zhonghuashoutao") at commercial maturity were stored at 0 °C and 20 °C. Firmness measurement and chemical analysis were performed at each storage time. In addition, three molecular imaging techniques, namely confocal Raman microspectroscopy (CRM), Fourier transform infrared microspectroscopy (FTIRM), and stimulated Raman scattering microscopy (SRS) were used to visualize changes in the spatial distribution of cell wall polysaccharides of peach fruit in a label-free way during the postharvest storage. The combination of CRM and FTIRM provided complementary spectral information to visualize the spatial changes of cellulose, hemicellulose, and pectin in the cell wall of peach flesh during softening at the single-cell level, and found that the cell wall polysaccharides tended to be concentrated in the cell corner of parenchymal cells at the late stage. Furthermore, SRS, which is an ultrafast Raman imaging technique (approximately three or four orders of magnitude faster than CRM), was used for high-throughput cell wall phenotypes measurement. Different degradation degrees of parenchymal cells during fruit softening were found based on the gray-scale statistical analysis of SRS data. In general, cell wall polysaccharides decreased during softening and tended to be concentrated in the cell corner for most parenchymal cells at the late stage, but there were also some cells not in line with the whole softening trends. The results show that there were differences in the content and spatial changes of cell wall polysaccharides among parenchymal cells of peach fruit during the softening process, and the hybrid use of CRM, FTIRM, and SRS is a promising method for simultaneous visualization of changes in cell wall polysaccharides of peach.

Insight into the relationship between S-lignin and fiber quality based on multiple research methods

Cotton (Gossypium hirsutum) is an important cash crop, providing people with high quality natural fiber. Lignin is the main component of cotton fiber, second only to cellulose. As a main substance filled in the cellulose framework during the secondary wall thickening process, lignin plays a key role in the formation of cotton fiber quality. However, the mechanism behind it is still unclear. In this research, we screened candidate genes involved in lignin biosynthesis based on analysis of cotton genome and transcriptome sequence data. The authenticity of the transcriptome data was verified by qRT-PCR assay. Total 62 genes were identified from nine gene families. In the process, we found the key gene GhCAD7 that affects the biosynthesis of S-lignin and the ratio of syringyl/guaiacyl (S/G). In addition, in combination with the metabolites and transcriptome profiles of the line 0-153 with high fiber quality and the line sGK9708 with low fiber quality during cotton fiber development, we speculate that the ratio of syringyl/guaiacyl (S/G) is inseparable from the quality of cotton fiber. Finally, the S-type lignin synthesis branch may play a more important role in the formation of high-quality fiber. This work provides insights into the synthesis of lignin in cotton and lays the foundation for future research into improving fiber quality.

Nitrate stimulation of N-Methylpyrrolidone biodegradation by Paracoccus pantotrophus: Metabolite mechanism and Genomic characterization

Due to the toxicological nature of N-methylpyrrolidone (NMP), the conventional anaerobic bioprocess is quite ineffective for NMP removal from wastewater. In order to achieve effective NMP biodegradation under anoxic condition, Paracoccus pantotrophus NJUST38 was isolated for the first time. The supplementation of nitrate into anoxic system resulted in complete removal of 5 mM NMP by NJUST38 within 11 h compared to 24% in the anaerobic control system in the absence of nitrate. Genome characterization revealed that NMP biodegradation catalyzed by several key enzymes/genes, including N-methylhydantoin amidohydrolase (hyuB), methyltransferase (cobA), 4-aminobutyrate-2-oxoglutarate transaminase (gabT), succinate-semialdehyde dehydrogenase (gabD) and so on. NMP biodegradation pathway was proposed based on several intermediates, where NMP was biodegraded mainly for providing electrons and reducing power to support microbial denitrification through tricarboxylic acid (TCA) cycle. The proposed mechanism should aid our mechanistic understanding of NMP biodegradation by Paracoccus pantotrophus and the development of sustainable bioremediation strategies.

Overexpression of Pear (Pyrus pyrifolia) CAD2 in Tomato Affects Lignin Content

PpCAD2 was originally isolated from the ‘Wangkumbae’ pear (Pyrus pyrifolia Nakai), and it encodes for cinnamyl alcohol dehydrogenase (CAD), which is a key enzyme in the lignin biosynthesis pathway. In order to verify the function of PpCAD2, transgenic tomato (Solanum lycopersicum) ‘Micro-Tom’ plants were generated using over-expression constructs via the agrobacterium-mediated transformation method. The results showed that the PpCAD2 over-expression transgenic tomato plant had a strong growth vigor. Furthermore, these PpCAD2 over-expression transgenic tomato plants contained a higher lignin content and CAD enzymatic activity in the stem, leaf and fruit pericarp tissues, and formed a greater number of vessel elements in the stem and leaf vein, compared to wild type tomato plants. This study clearly indicated that overexpressing PpCAD2 increased the lignin deposition of transgenic tomato plants, and thus validated the function of PpCAD2 in lignin biosynthesis.

In Silico Genome-Wide Analysis of Respiratory Burst Oxidase Homolog (RBOH) Family Genes in Five Fruit-Producing Trees, and Potential Functional Analysis on Lignification of Stone Cells in Chinese White Pear

: The accumulation of lignin in fruit has a significant negative impact on the quality of fruit-producing trees, and in particular the lignin formation stimulates the development of stone cells in pear fruit. Reactive oxygen species (ROS) are essential for lignin polymerization. However, knowledge of the RBOH family, a key enzyme in ROS metabolism, remains unknown in most fruit trees. In this study, a total of 40 RBOHs were identified from five fruit-producing trees (Pyrusbretschneideri, Prunuspersica, Citrussinensis, Vitisvinifera, and Prunusmume), and 10 of these sequences came from Pyrusbretschneideri. Multiple sequence alignments revealed that all 10 PbRBOHs contained the NADPH_Ox domain and the six alpha-helical transmembrane domains (TM-I to TM-VI). Chromosome localization and interspecies phylogenetic tree analysis showed that 10 PbRBOHs irregularly distributed on 8 chromosomes and 3 PbRBOHs (PbRBOHA, PbRBOHB, and PbRBOHD) are closely related to known lignification-related RBOHs. Furthermore, hormone response pattern analysis showed that the transcription of PbRBOHs is regulated by SA, ABA and MeJA. Reverse transcription-quantitative real-time polymerase chain reaction (qRT-PCR) and transcriptome sequencing analysis showed that PbRBOHA, PbRBOHB, and PbRBOHD accumulated high transcript abundance in pear fruit, and the transcriptional trends of PbRBOHA and PbRBOHD was consistent with the change of stone cell content during fruit development. In addition, subcellular localization revealed that PbRBOHA and PbRBOHD are distributed on the plasma membrane. Combining the changes of apoplastic superoxide (O2.-) content and spatio-temporal expression analysis, these results indicate that PbRBOHA and PbRBOHD, which are candidate genes, may play an important role in ROS metabolism during the lignification of pear stone cells. This study not only provided insight into the molecular characteristics of the RBOH family in fruit-producing trees, but also lays the foundation for studying the role of ROS in plant lignification.