scholarly journals Transcriptomic Analysis Reveals the Molecular Adaptation of Three Major Secondary Metabolic Pathways to Multiple Macronutrient Starvation in Tea (Camellia sinensis)

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 241 ◽  
Author(s):  
Hui Su ◽  
Xueying Zhang ◽  
Yuqing He ◽  
Linying Li ◽  
Yuefei Wang ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Element Analysis ◽  
Cis Element ◽  
Yield And Quality ◽  
Tea Quality ◽  
Function Enrichment Analysis ◽  
Tea Plants ◽  
Function Enrichment

Tea (Camellia sinensis (L.) O. Kuntze) is a widely consumed beverage. Lack of macronutrients is a major cause of tea yield and quality losses. Though the effects of macronutrient starvation on tea metabolism have been studied, little is known about their molecular mechanisms. Hence, we investigated changes in the gene expression of tea plants under nitrogen (N), phosphate (P), and potassium (K) deficient conditions by RNA-sequencing. A total of 9103 differentially expressed genes (DEG) were identified. Function enrichment analysis showed that many biological processes and pathways were common to N, P, and K starvation. In particular, cis-element analysis of promoter of genes uncovered that members of the WRKY, MYB, bHLH, NF-Y, NAC, Trihelix, and GATA families were more likely to regulate genes involved in catechins, l-theanine, and caffeine biosynthetic pathways. Our results provide a comprehensive insight into the mechanisms of responses to N, P, and K starvation, and a global basis for the improvement of tea quality and molecular breeding.

scholarly journals Integrative Analysis of Three Novel Competing Endogenous RNA Biomarkers with a Prognostic Value in Lung Adenocarcinoma

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Juan Tan ◽  
Weimin Wang ◽  
Bin Song ◽  
Yingjian Song ◽  
Zili Meng
Keyword(s):  
High Risk ◽  
Lung Adenocarcinoma ◽  
Prognostic Value ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Cerna Network ◽  
Kaplan Meier ◽  
Function Enrichment Analysis ◽  
Pathway Function ◽  
Function Enrichment

Increasing evidence has shown competitive endogenous RNAs (ceRNAs) play key roles in numerous cancers. Nevertheless, the ceRNA network that can predict the prognosis of lung adenocarcinoma (LUAD) is still lacking. The aim of the present study was to identify the prognostic value of key ceRNAs in lung tumorigenesis. Differentially expressed (DE) RNAs were identified between LUAD and adjacent normal samples by limma package in R using The Cancer Genome Atlas database (TCGA). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway function enrichment analysis was performed using the clusterProfiler package in R. Subsequently, the LUAD ceRNA network was established in three steps based on ceRNA hypothesis. Hub RNAs were identified using degree analysis methods based on Cytoscape plugin cytoHubba. Multivariate Cox regression analysis was implemented to calculate the risk score using the candidate ceRNAs and overall survival information. The survival differences between the high-risk and low-risk ceRNA groups were determined by the Kaplan-Meier and log-rank test using survival and survminer package in R. A total of 2,989 mRNAs, 185 lncRNAs, and 153 miRNAs were identified. GO and KEGG pathway function enrichment analysis showed that DE mRNAs were mainly associated with “sister chromatid segregation,” “regulation of angiogenesis,” “cell adhesion molecules (CAMs),” “cell cycle,” and “ECM-receptor interaction.” LUAD-related ceRNA network was constructed, which comprised of 54 nodes and 78 edges. Top ten hub RNAs (hsa-miR-374a-5p, hsa-miR-374b-5p, hsa-miR-340-5p, hsa-miR-377-3p, hsa-miR-21-5p, hsa-miR-326, SNHG1, RALGPS2, and PITX2) were identified according to their degree. Kaplan-Meier survival analyses demonstrated that hsa-miR-21-5p and RALGPS2 had a significant prognostic value. Finally, we found that a high risk of three novel ceRNA interactions (SNHG1-hsa-miR-21-5p-RALGPS2, SNHG1-hsa-miR-326-RALGPS2, and SNHG1-hsa-miR-377-3p-RALGPS2) was positively associated with worse prognosis. Three novel ceRNAs (SNHG1-hsa-miR-21-5p-RALGPS2, SNHG1-hsa-miR-326-RALGPS2, and SNHG1-hsa-miR-377-3p-RALGPS2) might be potential biomarkers for the prognosis and treatment of LUAD.

Identification of novel QTL for black tea quality traits and drought tolerance in tea plants (Camellia sinensis)

2018 ◽  
Vol 14 (1) ◽  
Author(s):  
Robert K. Koech ◽  
Pelly M. Malebe ◽  
Christopher Nyarukowa ◽  
Richard Mose ◽  
Samson M. Kamunya ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Camellia Sinensis ◽  
Black Tea ◽  
Quality Traits ◽  
Tea Quality ◽  
Tea Plants

scholarly journals Plant Availability of Magnesium in Typical Tea Plantation Soils 

2020 ◽  
Author(s):  
Qunfeng Zhang ◽  
Dandan Tang ◽  
Xiangde Yang ◽  
Saipan Geng ◽  
Ying He ◽  
...  
Keyword(s):  
Quality Improvement ◽  
Tea Plant ◽  
Tea Plantation ◽  
Fertilizer Use Efficiency ◽  
Fertilizer Use ◽  
Plant Cultivation ◽  
Yield And Quality ◽  
Tea Quality ◽  
Use Efficiency ◽  
Tea Plants

Abstract Background and aims: Magnesium (Mg) plays important roles in improving the yield and quality of tea. However, Mg deficiency frequently occurs in acidic tea plantation soil. Methods: Tea plants were pot-cultivated in 12 typical tea plantations soils amended with and without Mg fertilizer. Exchangeable Mg (Ex-Mg) concentration in soils were quantitatively extracted using four extraction solutions (Mehlich-3, BaCl2, CaCl2 and NH4OAC). Plant availability of Mg was evaluated by Mg uptake and use efficiency, as well as its association with quality-components in tea plants.Results: Ex-Mg in soils were extracted most efficiently by Mehlich-3, while Mg concentrations in tea plant tissue higher correlated with Ex-Mg extracted by CaCl2 than other extraction solutions. Mg fertilizer use efficiency in tea plant varied from 6.08% to 29.56 %, and Mg fertilization significantly improve green tea quality by decreasing the ratio of total polyphenol to amino acid in tea leaves (24-60%). Moreover, the effect of Mg application on tea quality improvement and the use efficiency of Mg fertilizer both negatively correlated with total Mg concentration (r = -0.94 and -0.63, respectively) and nitrogen (N) level (r = -0.61 and -0.51, respectively) in soils prior to tea plant cultivation.Conclusions: CaCl2 could be recommended for plant-available Mg extraction in tea plantation soil, and Mg fertilizer use efficiency could be affected and predicted by total N and Mg status in soils prior to tea plant cultivation, providing a potential theoretical for guidance of Mg fertilization for tea yield and quality improvement in tea plantation management.

scholarly journals The complexity and robustness of gene network inside the story between miRNAs and splicing isoforms in sacred lotus

2019 ◽  
Author(s):  
Yue Zhang ◽  
Razgar Seyed Rahmani ◽  
Xingyu Yang ◽  
Jinming Chen ◽  
Tao Shi
Keyword(s):  
Gene Network ◽  
Molecular Mechanisms ◽  
Functional Divergence ◽  
Enrichment Analysis ◽  
Flowering Plant ◽  
Transcript Isoforms ◽  
Function Enrichment Analysis ◽  
Splicing Isoforms ◽  
Gene Inhibition ◽  
Mrna Transcriptome

Abstract BACKGROUND. Gene expression is complex and regulated by multiple molecular mechanisms, such as miRNA-mediated gene inhibition and alternative-splicing of pre-mRNAs. However, coordination of interaction between miRNAs with different splicing isoforms, and the role of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus ( Nelumbo nucifera ), an economically important flowering plant. RESULTS. Through RNA-seq expression analyses among six lotus tissues, the negative regulatory roles of most miRNAs are reflected by their tissue-biased expression and the negative correlation with their targets in expression. Further, the central roles of miRNAs in the gene network was unveiled as there are more frequent interactions between miRNAs and hub isoforms than between miRNAs and non-hub isoforms. Surprisingly, for many genes, their corresponding isoforms were assigned to different co-expressed modules, and they exhibited more divergent mRNA structures including presence and absence of miRNA binding sites, suggesting functional divergence for many isoforms is escalated by both structural and expression divergence. The gene function enrichment analysis of miRNA targeted reveals that miRNAs are involved in regulation of lotus growth and development by regulating plant hormone-related pathway genes. CONCLUSION. Taken together, we carry out a comprehensive and deep analysis between miRNA and mRNA transcriptome to study coordination of interaction between miRNAs with different splicing isoforms. Our study on lotus highlights not only the complicate interactions between the miRNAs and transcript isoforms but also functional divergence of many transcript isoforms from the same locus in plant.

scholarly journals Tea plant genomics: achievements, challenges and perspectives

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
En-Hua Xia ◽  
Wei Tong ◽  
Qiong Wu ◽  
Shu Wei ◽  
Jian Zhao ◽  
...  
Keyword(s):  
Cultural Values ◽  
Molecular Mechanisms ◽  
Tea Plant ◽  
Plant Genome ◽  
Alcoholic Beverages ◽  
Plant Genomics ◽  
Breeding Programs ◽  
Tea Quality ◽  
Genomic Studies ◽  
Tea Plants

AbstractTea is among the world’s most widely consumed non-alcoholic beverages and possesses enormous economic, health, and cultural values. It is produced from the cured leaves of tea plants, which are important evergreen crops globally cultivated in over 50 countries. Along with recent innovations and advances in biotechnologies, great progress in tea plant genomics and genetics has been achieved, which has facilitated our understanding of the molecular mechanisms of tea quality and the evolution of the tea plant genome. In this review, we briefly summarize the achievements of the past two decades, which primarily include diverse genome and transcriptome sequencing projects, gene discovery and regulation studies, investigation of the epigenetics and noncoding RNAs, origin and domestication, phylogenetics and germplasm utilization of tea plant as well as newly developed tools/platforms. We also present perspectives and possible challenges for future functional genomic studies that will contribute to the acceleration of breeding programs in tea plants.

Identification and Validation of Glomerulotubular Crosstalk Genes Mediating IgA Nephropathy by Integrated Bioinformatics

2021 ◽  
Author(s):  
Yawen Bai ◽  
Yajing Li ◽  
Yali Xi ◽  
Chunjie Ma
Keyword(s):  
Enrichment Analysis ◽  
Gene Expression Omnibus ◽  
Diagnostic Significance ◽  
Function Enrichment Analysis ◽  
Gene Modules ◽  
Key Genes ◽  
End Stage ◽  
Microarray Datasets ◽  
Geo Database ◽  
Function Enrichment

Abstract BackgroundIgA nephropathy (IgAN), which has been reported as the most prevalent glomerulonephritis globally, is the major contributor to end-stage renal illness. This bioinformatics study aimed to explore glomeruli-tubulointerstitial crosstalk genes and dysregulated pathways relating to the pathogenesis of IgAN. MethodsThe microarray datasets from the Gene Expression Omnibus (GEO) database were searched. Weighted gene co-expression network analysis (WGCNA) and differentially expressed genes (DEGs) of both glomeruli and tubulointerstitial were conducted individually. The co-expression gene modules of tubulointerstitial and glomeruli were compared via gene function enrichment analysis. Subsequently, the crosstalk co-expression network was constructed via the STRING database and key genes were mined from the crosstalk network. Results583 DEGs and eight modules were identified in glomeruli samples, while 272 DEGs and four modules were in tubulointerstitial samples. There were 119 overlapping DEGs of the two groups. Among the distinctive modules, four modules in glomeruli and one module in tubulointerstitial were positively associated with IgAN. While four modules in glomeruli and two modules in tubulointerstitial were negatively associated with IgAN. The top ten key genes screened by CytoHubba were ITGAM, ALB, TYROBP, ITGB2, CYBB, HCK, CSF1R, LAPTM5, FN1and CTSS. The above genes were all validated using another two datasets, and all of the key genes demonstrated possible diagnostic significance. Conclusionshe crosstalk genes confirmed in this study may provide novel insight into the pathogenesis of IgAN. Immune-related pathways are associated with both glomerular and tubulointerstitial injuries in IgAN. The glomerulotubular crosstalk might perform a role in the pathogenesis of IgAN.

scholarly journals Construction of a circRNA-miRNA-mRNA Regulatory Network Reveals Potential Mechanism and Treatment Options for Osteosarcoma

2021 ◽  
Vol 12 ◽  
Author(s):  
Yi He ◽  
Haiting Zhou ◽  
Wei Wang ◽  
Haoran Xu ◽  
Hao Cheng
Keyword(s):  
Mrna Expression ◽  
Regulatory Network ◽  
Prognostic Value ◽  
Expression Profiles ◽  
Treatment Options ◽  
Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Primary Bone Tumor ◽  
Function Enrichment Analysis ◽  
Function Enrichment

BackgroundOsteosarcoma is a common malignant primary bone tumor in adolescents and children. Numerous studies have shown that circRNAs were involved in the proliferation and invasion of various tumors. However, the role of circRNAs in osteosarcoma remains unclear. Here, we aimed to explore the regulatory network among circRNA-miRNA-mRNA in osteosarcoma.MethodsThe circRNA (GSE140256), microRNA (GSE28423), and mRNA (GSE99671) expression profiles of osteosarcoma were collected from the Gene Expression Omnibus (GEO) database. Differentially expressed circRNAs, miRNAs and mRNAs were identified. CircRNA-miRNA interactions and miRNA-mRNA interactions were determined by Circular RNA Interactome (CircInteractome) database and microRNA Data Integration Portal (mirDIP) database, respectively. Then, we constructed a regulatory network. Function enrichment analysis of miRNA and mRNA was performed by DIANA-miRPath v3.0 and Metascape database, respectively. mRNAs with significant prognostic value were identified based on expression profiles from The Cancer Genome Atlas (TCGA) database, and we constructed a subnetwork for them. To make the most of the network, we used the CLUE database to predict potential drugs for the treatment of osteosarcoma based on mRNA expression in the network. And we used the STITCH database to analyze and validate the interactions among these drugs and mRNAs, and to further screen for potential drugs.ResultsA total of 9 circRNAs, 19 miRNAs, 67 mRNAs, 54 pairs of circRNA-miRNA interactions and 110 pairs of miRNA-mRNA interactions were identified. A circRNA-miRNA-mRNA network was constructed. Function enrichment analysis indicated that these miRNAs and mRNAs in the network were involved in the process of tumorigenesis and immune response. Among these mRNAs, STC2 and RASGRP2 with significantly prognostic value were identified, and we constructed a subnetwork for them. Based on mRNA expression in the network, three potential drugs, quinacridine, thalidomide and zonisamide, were screened for the treatment of osteosarcoma. Among them, quinacridine and thalidomide have been proved to have anti-tumor effects in previous studies, while zonisamide has not been reported. And a corresponding drug-protein interaction network was constructed.ConclusionOverall, we constructed a circRNA-miRNA-mRNA regulatory network to investigate the possible mechanism in osteosarcoma, and predicted that quinacridine, thalidomide and zonisamide could be potential drugs for the treatment of osteosarcoma.

scholarly journals Screening of disorders associated with osteosarcoma by integrated network analysis

2019 ◽  
Vol 39 (5) ◽  
Author(s):  
Yongfeng Dou ◽  
Kai Zhu ◽  
Zhaozhong Sun ◽  
Xiaopeng Geng ◽  
Qingmin Fang
Keyword(s):  
Network Analysis ◽  
Treatment Options ◽  
Enrichment Analysis ◽  
Integrated Network ◽  
Function Enrichment Analysis ◽  
Different Types ◽  
Endogenous Genes ◽  
Regulatory Effects ◽  
Function Enrichment

AbstractOsteosarcoma is a common malignant bone tumor in children and adolescents under the age of 20. However, research on the pathogenesis and treatment of osteosarcoma is still insufficient. In the present study, based on gene-phenotype correlation network, an analysis was performed to screen disorders related to osteosarcoma. First, we analyzed the differential expression of osteosarcoma in two groups according to different types of osteosarcoma and screened the differentially expressed genes (DEGs) related to osteosarcoma. Further, these DEG coexpression modules were obtained. Finally, we identified a series of regulatory factors, such as endogenous genes, transcription factors (TFs), and ncRNAs, which have potential regulatory effects on osteosarcoma, based on the prediction analysis of related network of gene phenotypes. A total of 3767 DEGs of osteosarcoma were identified and clustered them into 20 osteosarcoma-related dysfunction modules. And there were 38 endogenous genes (including ARF1, HSP90AB1, and TUBA1B), 53 TFs (including E2F1, NFKB1, and EGR1), and 858 ncRNAs (including MALAT1, miR-590-3p, and TUG1) were considered as key regulators of osteosarcoma through a series of function enrichment analysis and network analysis. Based on the results of the present study, we can show a new way for biologists and pharmacists to reveal the potential molecular mechanism of osteosarcoma typing, and provide valuable reference for different follow-up treatment options.

scholarly journals Tissue-Dependent Variation Profiles of Tea Quality-Related Metabolites in New Shoots of Tea Accessions

2021 ◽  
Vol 8 ◽  
Author(s):  
Hiroto Yamashita ◽  
Hideyuki Katai ◽  
Toshiyuki Ohnishi ◽  
Akio Morita ◽  
Sanjib Kumar Panda ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Dense Network ◽  
Accumulation Pattern ◽  
Specialized Metabolites ◽  
Chemical Indicators ◽  
Tea Quality ◽  
Genetic Mechanisms ◽  
Metabolic Variation ◽  
Tea Plants ◽  
Selection Of

Several metabolites define tea quality in new tea shoots composed of leaf and stem. To improve tea quality for breeding, it is important to understand the tissue-dependent genetic mechanisms and metabolic network responsible for the profile of tea quality-related metabolites. We analyzed the volatiles and specialized metabolites as the tea quality-related metabolites in leaves and stems of new shoots in 30 tea accessions to understand the tissue variation and network between tea quality-related metabolites. Our results provided the tissue-dependent variation network in the tea quality-related metabolites, including volatiles in new leaves and stems in tea accessions. Each volatile content in tea accessions showed the coefficient of variation ranging from 58.7 to 221.9% and 54.2 to 318.3% in new leaves and new stems, respectively. The accumulation pattern of tea quality-related metabolites in new leaves and stems varied depending on the accession. When comparing tea genetic populations, the profile of tea quality-related metabolites of new leaves, but not new stems, was the key to distinguishing tea genetic populations by chemical indicators. We described the network between tea quality-related metabolites, especially the dense network in new leaves. These results also will provide the key information for metabolic engineering and the selection of breeding materials in tea plants based on the tea quality-related metabolites and aid in understanding their molecular mechanisms and network of metabolic variation.

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