scholarly journals Transcriptome Profiling Reveals Potential Genes Involved in Browning of Fresh-cut Eggplant (Solanum Melongena L.)

2020 ◽  
Author(s):  
Xiaohui Liu ◽  
Jing Shang ◽  
Aidong Zhang ◽  
Zongwen Zhu ◽  
Dingshi Zha ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Fruits And Vegetables ◽  
Molecular Mechanisms ◽  
Solanum Melongena ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Enzymatic Browning ◽  
Fruit Samples ◽  
Phenylpropanoid Biosynthesis ◽  
Fresh Cut

Abstract Background: Fresh-cut processing promotes enzymatic browning of fresh fruits and vegetables, which negatively affects the appearance of products and impacts their nutrition. We used the RNA-Seq technique to analyze the transcriptomic changes occurring during the browning of fresh-cut eggplant (Solanum melongena L.) fruit samples from a browning-sensitive cultivar and a browning-resistant cultivar to investigate the genes and molecular mechanisms involved in browning. Results: A total of 111.55 GB of high-quality reads were generated, the genomes of each sample were compared, and 83.50%–95.14% of the data was mapped to the eggplant reference genome. Furthermore, a total of 19631 differentially expressed genes were identified, among which 12 genes and two WRKY transcription factors were identified as potentially involved in enzymatic browning in fresh-cut eggplant fruit. Moreover, the 14 differentially expressed genes associated with browning were verified using qRT-PCR. Conclusions: Several genes associated with phenolic oxidation, phenylpropanoid biosynthesis, and flavonoid biosynthesis were found to be differentially regulated between the eggplant cultivars with different browning sensitivities. This work is of great theoretical significance, as it provides a basis for future molecular studies and improvement of eggplants, and lays a theoretical foundation for the development of browning-resistant fresh-cut fruits and vegetables.

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

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xiaohui Liu ◽  
Aidong Zhang ◽  
Jie Zhao ◽  
Jing Shang ◽  
Zongwen Zhu ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Fruits And Vegetables ◽  
Molecular Mechanisms ◽  
Solanum Melongena ◽  
Transcriptome Profiling ◽  
Gene Families ◽  
Enzymatic Browning ◽  
Specific Expression ◽  
Fruit Samples ◽  
Fresh Cut

AbstractFresh-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.

Comparative transcriptome analysis identifies jasmonic pathway genes related to anther dehiscence in Solanum melongena L.

2020 ◽  
Author(s):  
Zhimin Wang ◽  
Shaowei Zhang ◽  
Chao Yuan ◽  
Yi Niu ◽  
Qinglin Tang ◽  
...  
Keyword(s):  
Male Sterility ◽  
Differentially Expressed Genes ◽  
Protein Interaction ◽  
Molecular Mechanisms ◽  
Solanum Melongena ◽  
Direct Interaction ◽  
Differentially Expressed ◽  
Anther Dehiscence ◽  
Interaction Studies ◽  
Pathway Analyses

Abstract Background: Anther indehiscence is an important form of functional male sterility that can facilitate the production of hybrid seeds. However, the molecular mechanisms of anther indehiscence-based male sterility in eggplant (Solanum melongena L.) have not been thoroughly explored. Therefore, we performed RNA-seq analysis to investigate the molecular mechanisms of anther dehiscence in eggplant. Results: We used transcriptome sequencing and qRT-PCR assays to compare the anthers of normally developing (F142) and anther indehiscent (S12) eggplant. We identified 2670 differentially expressed genes between lines. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses identified 31 differentially expressed genes related to hormone biosynthesis. We therefore measured the contents of the phytohormones jasmonic acid (JA), IAA, GA3 and ABA in S12 and F142. There were no significant differences in IAA, GA3 or ABA levels between S12 and F142. However, JA levels were significantly lower in S12 than in F142. Five key genes in the JA signaling pathway were differentially expressed in S12 vs. F142. Of these, SmJAZ and SmJAR-like were significantly up-regulated and SmDAD1, SmLOX and SmCOI1 were down-regulated in S12 vs. F142. In DNA-protein interaction studies, SmLOX, SmAOC, SmOPR3, SmCOI1 and SmJAZ1 failed to be enriched on the chromatin of SmDAD1. Protein–protein interaction studies identified a direct interaction between SmDAD1 and SmLOX, but SmDAD1 failed to interact with SmAOC, SmOPR3, SmCOI1 and SmJAZ1. Conclusion: JA is an essential factor affecting anther dehiscence in eggplant. SmDAD1 interacts with SmLOX to alter JA levels, thereby regulating anther dehiscence. Our data represent a valuable resource for further exploring the regulatory mechanisms underlying anther dehiscence in eggplant.

scholarly journals Comprehensive analysis of differential expression profiles via transcriptome sequencing in SH-SY5Y cells infected with CV-A16

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241174
Author(s):  
Yajie Hu ◽  
Zhen Yang ◽  
Shenglan Wang ◽  
Danxiong Sun ◽  
Mingmei Zhong ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Sequencing ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Control Group ◽  
Protein Coding ◽  
Qrt Pcr ◽  
Protein Coding Genes

Coxsackievirus A16 (CV-A16) is one of the viruses that is most frequently associated with hand-foot-and-mouth disease (HFMD). Previous studies have shown that CV-A16 infections are mostly self-limiting, but in recent years, it has been gradually found that CV-A16 infections can also induce neurological complications and eventually cause death in children with HFMD. Moreover, no curative drugs or preventative vaccines have been developed for CV-A16 infection. Therefore, it is particularly important to investigate the mechanism of CV-A16 infection-induced neuropathy. In the current study, transcriptome sequencing technology was used to identify changes in the transcriptome of SH-SY5Y cells infected with CV-A16, which might hide the mechanism of CV-A16-induced neuropathology. The transcriptome profiling showed that 82,406,974, 108,652,260 and 97,753,565 clean reads were obtained in the Control, CV-A16-12 h and CV-A16-24 h groups, respectively. And it was further detected that a total of 136 and 161 differentially expressed genes in CV-A16-12 h and CV-A16-24 h groups, respectively, when compared with Control group. Then, to explore the mechanism of CV-A16 infection, we focused on the common differentially expressed genes at different time points of CV-A16 infection and found that there were 34 differentially expressed genes based on which clustering analysis and functional category enrichment analysis were performed. The results indicated that changes in oxidation levels were particularly evident in the GO term analysis, while only the “Gonadotropin-releasing hormone receptor pathway” was enriched in the KEGG pathway analysis, which might be closely related to the neurotoxicity caused by CV-A16 infection. Meanwhile, the ID2 closely related to nervous system has been demonstrated to be increased during CV-A16 infection. Additionally, the data on differentially expressed non-protein-coding genes of different types within the transcriptome sequencing results were analyzed, and it was speculated that these dysregulated non-protein-coding genes played a pivotal role in CV-A16 infection. Ultimately, qRT-PCR was utilized to validate the transcriptome sequencing findings, and the results of qRT-PCR were in agreement with the transcriptome sequencing data. In conclusion, transcriptome profiling was carried out to analyze response of SH-SY5Y cells to CV-A16 infection. And our findings provide important information to elucidate the possible molecular mechanisms which were linked to the neuropathogenesis of CV-A16 infection.

scholarly journals Comparative Transcriptomic Analyses Provide Insights into the Enzymatic Browning Mechanism of Fresh-Cut Sand Pear Fruit

Horticulturae ◽  
2021 ◽  
Vol 7 (11) ◽  
pp. 502
Author(s):  
Jing Fan ◽  
Wei Du ◽  
Qi-Liang Chen ◽  
Jing-Guo Zhang ◽  
Xiao-Ping Yang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Transcript Level ◽  
Enzymatic Browning ◽  
Rna Seq ◽  
Pear Fruit ◽  
Total Polyphenol ◽  
Phenylpropanoid Biosynthesis ◽  
Key Enzyme ◽  
Fresh Cut ◽  
High Level

Pear (Pyrus spp.) is one of the most commonly consumed temperate fruits, having considerable economic and health importance. Fresh-cut or processed pear fruits are prone to browning because of the abundant phenolic compounds; however, little is known about the molecular mechanisms underlying enzymatic browning of fresh-cut sand pear fruit. In this study, fruits of two sand pear genotypes (low browning cultivar ‘Eli No.2′ and high browning cultivar ‘Weiningdahuangli’) were used to analyze the molecular mechanism of enzymatic browning by SMRT-seq and RNA-seq. The results generated 69,122 consensus isoforms, 21,336 new transcripts, 7105 alternative splicing events, and 254 long non-coding RNAs (lncRNAs). Furthermore, five genes related to enzymatic browning were predicted to be targets of six lncRNAs, and 9930 differentially expressed genes (DEGs) were identified between two different flesh browning cultivars. Meanwhile, most DEGs (e.g., PAL, 4CL, CAD, CCR, CHS, and LAR) involved in the phenylpropanoid biosynthesis pathway were up-regulated, and the expression of PPO and POD were highly expressed in the high-browning cultivar. Interestingly, the transcript level of PbrPPO4 (Pbr000321.4) was significantly higher than other PPO and POD genes, and a high level of total polyphenol and PPO activity were observed in the high browning cultivar. We found that the expression of lncRNA PB.156.1 was significantly positively correlated with the target gene PbrPPO4 (Pbr000321.4). The results suggest that PbrPPO4 might act as a major contributor and a key enzyme encoding gene in regulating fresh-cut sand pear fruit enzymatic browning; the expression of PbrPPO4 was probably regulated by lncRNA PB.156.1. Altogether, the transcriptomic and physiological analyses expand the knowledge of sand pear flesh enzymatic browning at the molecular level and provide a foundation for germplasm resources for molecular breeding of high polyphenol and low browning cultivars in sand pears.

Transcriptome profiling of differentially expressed genes of male and female inflorescences in spinach (Spinacia oleracea L.)

Genome ◽  
2021 ◽  
Author(s):  
Zhiyuan Liu ◽  
Haoying Wang ◽  
Zhaosheng Xu ◽  
Helong Zhang ◽  
Guoliang Li ◽  
...  
Keyword(s):  
Sex Determination ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Spinacia Oleracea ◽  
Transcriptome Profiling ◽  
Vital Role ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Male And Female ◽  
Spinacia Oleracea L

Spinach (Spinacia oleracea L.) is commonly considered a dioecious plant with heterogametic (XY) and homogametic (XX) sex chromosomes. The characteristic is also utilized for the production of spinach hybrid seeds. However, the molecular mechanisms of sex determination in spinach are still unclear because of a lack of genomic and transcriptomic information. In this study, RNA-sequencing (RNA-seq) was performed in male and female inflorescences to provide insight into the molecular basis of sex determination in spinach. Comparative transcriptome analyses showed that 2,278 differentially expressed genes (DEGs) were identified between male and female inflorescences. A high correlation between the RNA-Seq and qRT-PCR validation for DEGs was observed. Among these, 182 DEGs were annotated to transcription factors including the MYB family protein, bHLH family, and MADS family, suggesting these factors might play a vital role in sex determination. Moreover, 26 DEGs related to flower development, including nine ABCE class genes, were detected. Expression analyses of hormone pathways showed that brassinosteroids may be key hormones related to sex determination in spinach. Overall, this study provides a large amount of DEGs related to sexual expression and lays a foundation for unraveling the regulatory mechanism of sex determination in spinach.

Genome-Wide Transcriptome Profiling of Human Trabecular Meshwork Cells Treated with TGF-β2.

2021 ◽  
Author(s):  
Breedge Callaghan ◽  
Karen Lester ◽  
Brian Lane ◽  
Xiaochen Fan ◽  
Katarzyna Goljanek-Whysall ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Pathology ◽  
Trabecular Meshwork ◽  
Transforming Growth Factor Beta ◽  
Molecular Mechanisms ◽  
Transforming Growth Factor ◽  
Open Angle Glaucoma ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Trabecular Meshwork Cells

Abstract Glaucoma is a complex neurodegenerative disease resulting in progressive optic neuropathy and is a leading cause of irreversible blindness worldwide. Primary open angle glaucoma (POAG) is the predominant form affecting 65.5 million people globally. Despite the prevalence of POAG and the identification of over 120 glaucoma related genetic loci, the underlaying molecular mechanisms are still poorly understood. The transforming growth factor beta (TGF-β) signalling pathway is implicated in the molecular pathology of POAG. To gain a better understanding of the role TGF-β2 plays in the glaucomatous changes to the molecular pathology in the trabecular meshwork, we employed RNA-Seq to delineate the TGF-β2 induced changes in the transcriptome of normal primary human trabecular meshwork cells (HTM). We identified a significant number of differentially expressed genes and associated pathways that contribute to the pathogenesis of POAG. The differentially expressed genes were predominantly enriched in ECM regulation, TGF-β signalling, proliferation/apoptosis, inflammation/wound healing, MAPK signalling, oxidative stress and RHO signalling. Canonical pathway analysis confirmed the enrichment of RhoA signalling, inflammatory-related processes, ECM and cytoskeletal organisation in HTM cells in response to TGF-β2. We also identified novel genes and pathways that were affected after TGF-β2 treatment in the HTM, suggesting additional pathways are activated, including Nrf2, PI3K-Akt, MAPK and HIPPO signalling pathways. The identification and characterisation of TGF-β2 dependent differentially expressed genes and pathways in HTM cells is essential to understand the patho-physiology of glaucoma and to develop new therapeutic agents.

scholarly journals Metabolomics Study of Browning Mechanism in Eggplant Fruits

2020 ◽  
Author(s):  
Xiaohui Liu ◽  
Shengmei Zhang ◽  
Jing Shang ◽  
Aidong Zhang ◽  
Zongwen Zhu ◽  
...  
Keyword(s):  
Chlorogenic Acid ◽  
Fruits And Vegetables ◽  
Solanum Melongena ◽  
Atp Synthesis ◽  
Pentose Phosphate ◽  
Enzymatic Browning ◽  
Glutathione Metabolism ◽  
Catering Industry ◽  
Metabolomics Study ◽  
Fresh Cut

Abstract Objective ： Fresh-cut fruits and vegetables is an emerging type of fruits and vegetables processing products for consumers to eat immediately or for the catering industry. Enzymatic browning is one of the crucial problems compromising the flavor and texture of fresh-cut fruit and vegetables. Eggplant is a common vegetable, which is favored by consumers. Accordingly, we used an untargeted metabolomics approach based on liquid chromatography-mass spectrometry (LC-MS) to explore the browning mechanism in peeled eggplant ( Solanum melongena L . ). Results: Metabolomics revealed several hundred differential metabolites, including lipids, phenols, sugars and fatty acids. The content of these metabolites changed dynamically as the peeled time increased. The content of polyphenols, especially chlorogenic acid, increased significantly, suggesting that the main substrate for enzymatic browning in eggplant is chlorogenic acid. Furthermore, all the differential metabolite were mapped to KEGG pathway, revealing significant differences in linoleic acid metabolism, tyrosine metabolism，glutathione metabolism, pentose phosphate pathway, tropane, piperidine and pyridine alkaloid biosynthesis, phenylpropanol metabolism and glycosylphosphatidylinositol(GPI)-anchor biosynthesis over time. Therefore, we speculate that some metabolic pathways that are closely connected with respiration, glycolysis, ATP synthesis, and phenolic synthesi are disturbed after peeling, under the action of enzymes, eventually leading to browning.

scholarly journals Metabolomics Study of Browning Mechanism in Eggplant Fruits

2019 ◽  
Author(s):  
Xiaohui Liu ◽  
Shengmei Zhang ◽  
Jing Shang ◽  
Aidong Zhang ◽  
Zongwen Zhu ◽  
...  
Keyword(s):  
Chlorogenic Acid ◽  
Fruits And Vegetables ◽  
Solanum Melongena ◽  
Atp Synthesis ◽  
Pentose Phosphate ◽  
Untargeted Metabolomics ◽  
Enzymatic Browning ◽  
Glutathione Metabolism ◽  
Catering Industry ◽  
Fresh Cut

Abstract Background: Fresh-cut fruits and vegetables is a emerging type of fruits and vegetables processing products for consumers to eat immediately or for the catering industry. Enzymatic browning is one of the crucial problems compromising the flavor and texture of fresh-cut fruit and vegetables. Eggplant is a common vegetable, which is favored by consumers. Accordingly, we used an untargeted metabolomics approach based on liquid chromatography-mass spectrometry (LC-MS) to explore the browning mechanism in peeled eggplant ( Solanum melongena L . ). Results: Metabolomics revealed several hundred differential metabolites, including lipids, phenols, sugars and fatty acids. The content of these metabolites changed dynamically as the peeled time increased. The content of polyphenols, especially chlorogenic acid, increased significantly, suggesting that the main substrate for enzymatic browning in eggplant is chlorogenic acid. Furthermore, all the differential metabolite were mapped to KEGG pathway, revealing significant differences in linoleic acid metabolism, tyrosine metabolism ，glutathione metabolism, pentose phosphate pathway, tropane, piperidine and pyridine alkaloid biosynthesis, phenylpropanol metabolism and glycosylphosphatidylinositol(GPI)-anchor biosynthesis over time. Therefore, we speculate that some metabolic pathways that are closely connected with respiration, glycolysis, ATP synthesis, and phenolic synthesi are disturbed after peeling, under the action of enzymes, eventually leading to browning. Conclusions: We established an untargeted metabolomics method based on LC-MS technology to explain the mechanism of eggplant browning, which may lay the foundation for better understanding the mechanism of browning during the fruits and vegetables deeply processing, and furnish new ideas and perspectives for understanding fruit and vegetable browning in the future.

Identification of Differentially Expressed Genes Associated with Papillary Thyroid Carcinoma

2020 ◽  
Vol 23 (6) ◽  
pp. 546-553
Author(s):  
Hongyuan Cui ◽  
Mingwei Zhu ◽  
Junhua Zhang ◽  
Wenqin Li ◽  
Lihui Zou ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Cellular Proliferation ◽  
Mrna Level ◽  
Thyroid Tissue ◽  
Differentially Expressed ◽  
Thyroid Tumors ◽  
Papillary Thyroid

Objective: Next-generation sequencing (NGS) was performed to identify genes that were differentially expressed between normal thyroid tissue and papillary thyroid carcinoma (PTC). Materials & Methods: Six candidate genes were selected and further confirmed with quantitative real-time polymerase chain reaction (qRT-PCR), and immunohistochemistry in samples from 24 fresh thyroid tumors and adjacent normal tissues. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was used to investigate signal transduction pathways of the differentially expressed genes. Results: In total, 1690 genes were differentially expressed between samples from patients with PTC and the adjacent normal tissue. Among these, SFRP4, ZNF90, and DCN were the top three upregulated genes, whereas KIRREL3, TRIM36, and GABBR2 were downregulated with the smallest p values. Several pathways were associated with the differentially expressed genes and involved in cellular proliferation, cell migration, and endocrine system tumor progression, which may contribute to the pathogenesis of PTC. Upregulation of SFRP4, ZNF90, and DCN at the mRNA level was further validated with RT-PCR, and DCN expression was further confirmed with immunostaining of PTC samples. Conclusion: These results provide new insights into the molecular mechanisms of PTC. Identification of differentially expressed genes should not only improve the tumor signature for thyroid tumors as a diagnostic biomarker but also reveal potential targets for thyroid tumor treatment.

scholarly journals Study on browning mechanism of fresh-cut eggplant (Solanum melongena L.) based on metabolomics, enzymatic assays and gene expression

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xiaohui Liu ◽  
Aidong Zhang ◽  
Jing Shang ◽  
Zongwen Zhu ◽  
Ye Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruits And Vegetables ◽  
Solanum Melongena ◽  
Downward Trend ◽  
Glutathione Metabolism ◽  
Phenylpropanoid Metabolism ◽  
Kegg Pathways ◽  
Maximum Value ◽  
Cut Time ◽  
Fresh Cut

AbstractEnzymatic browning is one of the crucial problems compromising the flavor and texture of fresh-cut fruit and vegetables. In this study, an untargeted metabolomics approach based on liquid chromatography-mass spectrometry (LC–MS) was used to explore the browning mechanism in fresh-cut eggplant. Metabolomics studies showed that with the increase of fresh-cut time, the contents of 946 metabolites changed dynamically. The metabolites having the same trend share common metabolic pathways. As an important browning substrate, the content of chlorogenic acid increased significantly, suggesting that may be more important to fresh-cut eggplant browning; all 119 common differential metabolites in 5 min/CK and 3 min/CK contrastive groups were mapped onto 31 KEGG pathways including phenylpropanol metabolism, glutathione metabolism pathway, et al. In physiological experiments, results showed that the Phenylpropanoid-Metabolism-Related enzymes (PAL, C4H, 4CL) were changed after fresh-cut treatment, the activities of three enzymes increased first and then decreased, and reached the maximum value at 5 min, indicating the accumulation of phenolic substances. At the same time, ROS were accumulated when plant tissue damaged by cutting, the activities of related antioxidant enzymes (SOD, APX and CAT) changed dynamically after oxidative damage. SOD and APX content increased significantly and reached the maximum value at 10 min after cutting, and then showed a downward trend. However, CAT activity increased sharply and reached the maximum value within 3 min after cutting, then maintained the same activity, and showed a downward trend after 30 min. These data fully demonstrated that the activities of browning related enzymes and gene expression increased with the prolonging of fresh cutting time. We explained the browning mechanism of fresh-cut eggplant by combining metabolomics and physiology, which may lay the foundation for better understanding the mechanism of browning during the fruits and vegetables during processing.

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