Transcription Profiles Reveal the Regulatory Synthesis of Phenols during the Development of Lotus Rhizome (Nelumbo nucifera Gaertn)

Identification of novel natural anti-browning agents based on phenotypic and metabolites differences in potato cultivars

This study aimed to elucidate the changes of browning-related metabolite in fresh-cut potato and to identify anti-browning agents. Metabolomics and weighted correlation network analysis (WGCNA) were used to identify metabolites and correlate them with potato browning traits. A total of 79 browning trait-positive-related metabolites and 19 browning trait-negative-related metabolites were obtained from four key modules via WGCNA. The accumulation of metabolites with rich reducing groups and acidic groups were found to enhance anti-browning activity in potatoes. Among these metabolites, only L-pyroglutamic acid (L-PA) and ascorbic acid had variable importance for the projection (VIP) values greater than 1.5. In addition, it was found that L-PA inhibited polyphenol oxidase (PPO) activity by lowering pH and interacting with amino acid residues of PPO. L-PA also inhibited the growth of microorganisms in fresh-cut potato. Our results show that L-AP is an effective novel anti-browning agent with antibacterial activity.

The storage quality and transcriptome analysis of fresh-cut taro by L-ascorbic acid combined with ultrasonic treatment

Fresh-cut taro, renowned for its high nutritional value and convenience, is prone to rapid browning post-cutting, which hinders its storage life. This study focused on the effects of L-ascorbic acid (AA) combined with ultrasound (US) treatment (AS) on the storage quality and transcriptome analysis of fresh-cut slices of Yongding June Red Taro. Compared to the control (CK) group, AS treatment effectively reduced the weight loss rate of taro slices, maintained higher hardness, delayed the increase of browning, and inhibited the accumulation of O2- and H2O2. Furthermore, the AS group showed increased glutathione levels and maintained higher activities of ascorbate peroxidase and glutathione reductase, yet decreased the contents of flavonoids and reducing sugars. Simultaneously, in the AS group, the activities of tyrosinase and lipoxygenase were lowered, thereby preserving the high sensory quality of fresh-cut taro slices. Transcriptome analysis revealed that differentially expressed genes (DEGs) between the AS and CK groups were annotated and categorized into 50 and 20 functional groups based on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. Notably, both groups exhibited significant enrichment in processes related to photosynthesis, protein processing in the endoplasmic reticulum, and isoflavone biosynthesis. Therefore, we concluded that AS treatment could alleviate oxidative stress and maintain storage quality by regulating metabolic pathways. These findings provide insights into the physiological changes occurring in taro immediately after cutting and serve as an essential basis for developing effective storage and preservation techniques.

Mechanism of exogenous methyl jasmonate in regulating the quality of fresh-cut Chinese water chestnuts

Fresh-cut Chinese water chestnuts (CWCs) are susceptible to yellowing and browning during storage due to mechanical damage and the loss of protective outer skin, adversely affecting their marketability and shelf life. Methyl jasmonate (MeJA) is currently extensively used for food preservation, but it has not been used in Chinese water chestnuts. This study investigated the effect of MeJA treatment on the quality of fresh-cut CWCs. Fresh-cut CWCs immersed in 20 μM MeJA solution for 10 min and stored at 10°C for 5 d effectively delayed the yellowing process, reduced the respiration rate, and minimized the weight and soluble solids loss during storage. In addition, MeJA treatment induced the activities of superoxide dismutase (SOD) and catalase (CAT), which improved the antioxidant capacity of fresh-cut CWCs and inhibited the generation of reactive oxygen species (ROS). Meanwhile, MeJA treatment inhibited the activities of phenylalanine aminotransferase (PAL), polyphenol oxidase (PPO) and peroxidase (POD). The results of quantitative real-time PCR (qRT-PCR) showed that MeJA down-regulated the expression of CwCHS1, CwCHS2, CwCHS3 and CwCHI2 in freshly cut CWCs and inhibited the accumulation of flavonoids, thus delaying the surface discoloration of freshly cut CWCs.

Profiles of phenolics and their synthetic pathways in Asparagus officinalis L

The synthetic pathways of some phenolics compounds in asparagus have been reported, however, the diversified phenolics compounds including their modification and transcription regulation remains unknown. Thus, multi-omics strategies were applied to detect the phenolics profiles, contents, and screen the key genes for phenolics biosynthesis and regulation in asparagus. A total of 437 compounds, among which 204 phenolics including 105 flavonoids and 82 phenolic acids were detected with fluctuated concentrations in roots (Rs), spears (Ss) and flowering twigs (Fs) of the both green and purple cultivars. Based on the detected phenolics profiles and contents correlated to the gene expressions of screened synthetic enzymes and regulatory TFs, a full phenolics synthetic pathway of asparagus was proposed for the first time, essential for future breeding of asparagus and scaled healthy phenolics production using synthetic biological strategies.

Preliminary Study on the Formation Mechanism of Malformed Sweet Cherry (Prunus avium L.) Fruits in Southern China Using Transcriptome and Metabolome Data

Gibberellin (GA) is an important plant hormone that is involved in various physiological processes during plant development. Sweet cherries planted in southern China have always encountered difficulty in bearing fruit. In recent years, gibberellin has successfully solved this problem, but there has also been an increase in malformed fruits. This study mainly explores the mechanism of malformed fruit formation in sweet cherries. By analyzing the synthesis pathway of gibberellin using metabolomics and transcriptomics, the relationship between gibberellin and the formation mechanism of deformed fruit was preliminarily determined. The results showed that the content of GA3 in malformed fruits was significantly higher than in normal fruits. The differentially expressed genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were mainly enriched in pathways such as "plant hormone signal transduction", "diterpenoid biosynthesis", and "carotenoid biosynthesis". Using Quantitative Real-Time Reverse Transcription PCR (qRT-PCR) analysis, the gibberellin hydrolase gene GA2ox and gibberellin synthase genes GA20ox and GA3ox were found to be significantly up-regulated. Therefore, we speculate that the formation of malformed fruits in sweet cherries may be related to the accumulation of GA3. This lays the foundation for further research on the mechanism of malformed sweet cherry fruits.

Transcriptomics and metabolomics provide insight into the anti-browning mechanism of selenium in freshly cut apples

Enzymatic browning has a considerable negative impact on the acceptability and marketability of freshly cut apples. However, the molecular mechanism by which selenium (Se) positively affects freshly cut apples in this regard is not yet clear. In this study, 0.75 kg/plant of Se-enriched organic fertilizer was applied to "Fuji" apple trees during the young fruit stage (M₅, May 25), the early fruit enlargement stage (M₆, June 25), and the fruit enlargement stage (M₇, July 25), respectively. The same amount of Se-free organic fertilizer was applied as a control. Herein, the regulatory mechanism by which exogenous Se exerts its anti-browning effect in freshly cut apples was investigated. The results showed that the M₇ treatment applied in Se-reinforced apples could remarkably inhibit their browning at 1 h after being freshly cut. Additionally, the expression of polyphenol oxidase (PPO) and peroxidase (POD) genes treated with exogenous Se was significantly reduced compared to controls. Moreover, the lipoxygenase (LOX) and phospholipase D (PLD) genes, which are involved in membrane lipid oxidation, were expressed at higher levels in the control. The gene expression levels of the antioxidant enzymes catalase (CAT), superoxide dismutase (SOD), glutathione S-transferase (GST), and ascorbate peroxidase (APX) were upregulated in the different exogenous Se treatment groups. Similarly, the main metabolites measured during the browning process were phenols and lipids; thus, it could be speculated that the mechanism by which exogenous Se produces its anti-browning effect may be by reducing phenolase activity, improving the antioxidant capacity of the fruits, and alleviating membrane lipid peroxidation. In summary, this study provides evidence regarding and insight into the response mechanism employed by exogenous Se to inhibit browning in freshly cut apples.

Nontarget Metabolites of Rhizomes of Edible Sacred Lotus Provide New Insights into Rhizome Browning

The “edible rhizome” variant of Nelumbo nucifera with various cultivars has a long history of use as a food in East Asia. In this study, 48 target metabolites were untargeted and identified in 212 rhizome cultivars (tropical and temperate types) using ultraperformance liquid chromatography-electrospray ionization quadrupole time-of-flight high-resolution mass spectrometry; among these, 32 compounds were newly reported in the rhizome. Combined with the browning phenotype of 212 lotus rhizomes, (epi) catechin, norarmepavine, and N-feruloyl-3-methoxytyramine were used as predominant chemical markers to separate different degrees of lotus rhizome browning. p-Coumaroyltyramine and N-trans-feruloyltyramine were selected as predominant chemical markers to investigate the differential expression between tropical and temperate lotus using principal component analysis and orthogonal partial least squares discriminant analysis. Shared and unique structure plots were used to compare the outcomes of the ecotype and browning OPLS model, showing that variation in tropical lotus rhizome browning is not obvious; this will be of great importance for genetic improvement by providing a hereditary basis.

Metabolomic Analysis, Combined with Enzymatic and Transcriptome Assays, to Reveal the Browning Resistance Mechanism of Fresh-Cut Eggplant

Browning has been the primary limitation in eggplant processing. This study investigates the molecular mechanism underlying fresh-cut eggplant fruit browning by observing the physicochemical characteristics of browning-resistant (‘F’) and browning-sensitive (‘36′) eggplant cultivars. Browning-related enzyme activity and gene expression (PPO, LOX, and PLD) were significantly higher in the ‘36′ eggplant, thereby enhancing the degree of browning, compared to the ‘F’ eggplant. The MDA content and O₂⁻ production rate progressively increased as browning increased, while the antioxidant capacity of the fruit decreased. The cutting injury significantly activated the expression of PAL, thereby inducing the accumulation of phenolic acids, while the PPO gene was significantly upregulated, which activated the activity of polyphenol oxidase. Our results showed that the oxidation of chlorogenic acids to chlorogenic quinones resulted in the occurrence of browning, which suggests chlorogenic acid as the main browning substrate in fresh-cut eggplant.

Transcriptome profiling reveals potential genes involved in browning of fresh-cut eggplant (Solanum melongena L.)

Fresh-cut processing promotes enzymatic browning of fresh fruits and vegetables, which negatively affects the product appearance and impacts their nutrition. We used RNA-sequencing to analyze the transcriptomic changes occurring during the browning of fresh-cut eggplant fruit samples from both browning-sensitive and browning-resistant cultivars to investigate the molecular mechanisms involved in browning. A total of 8347 differentially expressed genes were identified, of which 62 genes were from six gene families (i.e., PPO, PAL, POD, CAT, APX, and GST) potentially associated with enzymatic browning. Furthermore, using qRT-PCR, we verified 231 differentially regulated transcription factors in fresh-cut eggplant fruits. The enzyme activities of PPO, POD, PAL, and CAT in '36' were significantly higher than those of 'F' fresh-cut for 15 min. Both PPO and POD play a major role in the browning of eggplant pulp and might therefore act synergistically in the browning process. Meanwhile, qPCR results of 18 browning related genes randomly screened in 15 eggplant materials with different browning tolerance showed variant-specific expression of genes. Lastly, gene regulatory networks were constructed to identify the browning-related genes. This work provides a basis for future molecular studies of eggplants, and lays a theoretical foundation for the development of browning-resistant fresh-cut fruits and vegetables.

Distinct methylome patterns contribute to ecotypic differentiation in the growth of the storage organ of a flowering plant (sacred lotus)

DNA methylation is an epigenetic modification involved in phenotypic diversity, plant development, and environmental responses. However, the mechanisms of DNA methylation underpinning the adaption of lotus (Nelumbo nucifera) ecotypes to high and low latitudes remain unsolved, especially adaptive evolution of their storage organs. Tropical and temperate lotus ecotypes have thin and enlarged rhizomes which are adapted to low and high latitudes, respectively. Here, we investigated the DNA methylomes and transcriptomes of rhizomes of the temperate and tropical lotus to address this issue. Compared with that of the tropical lotus, the DNA of the temperate lotus was significantly more hypermethylated, indicating an increase in global DNA methylation in the lotus, with rhizome enlargement. Meanwhile, genes associated with differentially methylated regions in their promoters tended to be differentially expressed between the two ecotypes. Interestingly, the genes with their expression negatively correlated with methylation levels in their promoters and genomic regions displayed significantly higher transposon coverage, while the genes showing a significant positive correlation between expression and methylation showed lesser transposon coverage. Further, we identified that DNA methylation, especially in the promoter region, was significantly correlated with the expression of many starch-biosynthetic, gibberellin-, and brassinosteroid-signalling genes associated with rhizome differentiation. Overall, our study unveiled that distinct global and local methylation patterns between the two lotus ecotypes contribute to their expression differences and adaptive phenotypic divergence of their storage organs, highlighting the role of DNA methylation in shaping the ecotypic differentiation of lotus.

Transcriptome Analysis of Gene Expression Profiles of Tomato Yellow Leaf Curl Virus-Infected Whiteflies over Different Viral Acquisition Access Periods

Tomato yellow leaf curl virus (TYLCV), which is transmitted by Bemisia tabaci in a persistent-circulative manner, threatens tomato production worldwide. Little is known about the complicated interaction during this process at the molecular level. In this study, viral AAPs at 0 h, 2 h, 6 h, 12 h and 48 h were investigated using a comparative transcriptome analysis to uncover the transcriptional responses of whiteflies to virus infection. Our results have shown that 755, 587, 1140 and 1347 differentially expressed genes (DEGs) were identified in the comparisons of the data of 0 h vs. 2 h, 0 h vs. 6 h, 0 h vs. 12 h and 0 h vs. 48 h, respectively. KEGG analysis showed that DEGs associated with metabolisms and signal transduction were down-regulated in virus-infected whiteflies. Additionally, 16 up-regulated putative transporter genes and 10 down-regulated genes associated with IL-17 signaling pathway were identified by time-associated gene cluster analysis. These data boost our comprehensions on whitefly-TYLCV interactions associated with different viral AAPs.

Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas

Background

Jatropha curcas, a tropical shrub, is a promising biofuel crop, which produces seeds with high content of oil and protein. To better understand the maturation process of J. curcas seeds and to improve its agronomic performance, a two-step approach was performed in six different maturation stages of seeds: 1) generation of the entire transcriptome of J. curcas seeds using 454-Roche sequencing of a cDNA library, 2) comparison of transcriptional expression levels using a custom Agilent 8x60K oligonucleotide microarray.

Results

A total of 793,875 high-quality reads were assembled into 19,382 unique full-length contigs, of which 13,507 could be annotated with Gene Ontology (GO) terms. Microarray data analysis identified 9111 probes (out of 57,842 probes), which were differentially expressed between the six maturation stages. The expression results were validated for 75 selected transcripts based on expression levels, predicted function, pathway, and length.

Result from cluster analyses showed that transcripts associated with fatty acid, flavonoid, and phenylpropanoid biosynthesis were over-represented in the early stages, while those of lipid storage were over-represented in the late stages. Expression analyses of different maturation stages of J. curcas seed showed that most changes in transcript abundance occurred between the two last stages, suggesting that the timing of metabolic pathways during seed maturation in J. curcas occurs in late stages. The co-expression results showed that the hubs (CB5-D, CDR1, TT8, DFR, HVA22) with the highest number of edges, associated with fatty acid and flavonoid biosynthesis, are showing a decrease in their expression during seed maturation. Furthermore, seed development and hormone pathways are significantly well connected.

Conclusion

The obtained results revealed differentially expressed sequences (DESs) regulating important pathways related to seed maturation, which could contribute to the understanding of the complex regulatory network during seed maturation with the focus on lipid, flavonoid and phenylpropanoid biosynthesis. This study provides detailed information on transcriptional changes during J. curcas seed maturation and provides a starting point for a genomic survey of seed quality traits. The results highlighted specific genes and processes relevant to the molecular mechanisms involved in Jatropha seed maturation. These data can also be utilized regarding other Euphorbiaceae species.

An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of Bagging and Non-Bagging "Golden Delicious" Apple

Apple skin russeting naturally occurs in many varieties, particularly in “Golden Delicious” and its pedigree, and is regarded as a non-invasive physiological disorder partly caused by excessive deposition of lignin. However, the understanding of its molecular mechanism is still limited. In this study, we used iTRAQ (isobaric tags for relative and absolute quantitation) and RNA-seq to detect the changes in the expression levels of genes and proteins in three developmental stages of russeting formation, in russeted (non-bagging) and non-russeted (bagging) skin of “Golden Delicious” apple. 2856 differentially expressed genes and 942 differentially expressed proteins in the comparison groups were detected at the transcript level and protein level, respectively. A correlation analysis of the transcriptomics and proteomics data revealed that four genes (MD03G1059200, MD08G1009200, MD17G1092400, and MD17G1225100) involved in lignin biosynthesis are significant changed during apple russeting formation. Additionally, 92 transcription factors, including 4 LIM transcription factors, may be involved in apple russeting formation. Among them, one LIM transcription factor (MD15G1068200) was capable of binding to the PAL-box like (CCACTTGAGTAC) element, which indicated it was potentially involved in lignin biosynthesis. This study will provide further views on the molecular mechanisms controlling apple russeting formation.