Ontology highlight
ABSTRACT:
PROVIDER: PRJNA385768 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We conducted a RNA-Seq analysis of MeJA-treated Chinese cabbage leaf transcriptome. Total 14,619,469 sequence reads were generated to produce 27,461 detected genes, among which 1,451 genes were up-regulated and 991 genes were down-regulated as differentially expressed genes (DEGs) (log2 ratio â¥1, false discovery rate â¤0.001). More than 90% of the DEGs (2,278) were between 1.0- and 3.0-fold (log2 ratio). The most highly represented pathways by 1,674 annotated DEGs were related to âmetabolic pathwaysâ (333 members), âribosomeâ (314 members), âbiosynthesis of secondary metabolitesâ (218 members), âplant-pathogen interactionâ (146 members), and âplant hormone signal transductionâ (99 members). Fourteen genes involved in JA biosynthesis pathway were up-regulated. As many as 182 genes for the biosynthesis of several secondary metabolites were induced, and the level of indole glucosinolate was highly increased by MeJA treatment. The genes encoding sugar catabolism and some amino acids synthesis were up-regulated, which could supply structural intermediates and energy for the biosynthesis of secondary metabolites. The results demonstrated a high degree of transcriptional complexity with dynamic coordinated changes in global gene expression of Chinese cabbage in response to MeJA treatment. It expands our understanding of the complex molecular events on JA-induced plant resistance and accumulation of secondary metabolites. It also provides a foundation for further studies on the molecular mechanisms of different pathways in other Brassica crops under MeJA treatment. Transcriptomic analysis of MeJA-treated Chinese cabbage leaf
2015-12-31 | E-GEOD-51363 | biostudies-arrayexpress
Project description:We conducted a RNA-Seq analysis of MeJA-treated Chinese cabbage leaf transcriptome. Total 14,619,469 sequence reads were generated to produce 27,461 detected genes, among which 1,451 genes were up-regulated and 991 genes were down-regulated as differentially expressed genes (DEGs) (log2 ratio ≥1, false discovery rate ≤0.001). More than 90% of the DEGs (2,278) were between 1.0- and 3.0-fold (log2 ratio). The most highly represented pathways by 1,674 annotated DEGs were related to “metabolic pathways” (333 members), “ribosome” (314 members), “biosynthesis of secondary metabolites” (218 members), “plant-pathogen interaction” (146 members), and “plant hormone signal transduction” (99 members). Fourteen genes involved in JA biosynthesis pathway were up-regulated. As many as 182 genes for the biosynthesis of several secondary metabolites were induced, and the level of indole glucosinolate was highly increased by MeJA treatment. The genes encoding sugar catabolism and some amino acids synthesis were up-regulated, which could supply structural intermediates and energy for the biosynthesis of secondary metabolites. The results demonstrated a high degree of transcriptional complexity with dynamic coordinated changes in global gene expression of Chinese cabbage in response to MeJA treatment. It expands our understanding of the complex molecular events on JA-induced plant resistance and accumulation of secondary metabolites. It also provides a foundation for further studies on the molecular mechanisms of different pathways in other Brassica crops under MeJA treatment.
2015-12-31 | GSE51363 | GEO
Project description:An increasing amount of evidence attest that the tea made by albino tea cultivars processes characteristic aroma and taste, which has been considered as a new potential product in the market. Therefore, flavor formation mechanism of albino tea cultivars have drawn exceeding attention from researchers. In this study, transcriptome, metabolomics, and whole-genome bisulfite sequencing (WGBS) were employed to investigate shading effects on leaf color conversion and biosynthesis of three major secondary metabolites in the Albino tea cultivar ‘Yujinxiang’. The increase of leaf chlorophyll level is the major cause of shaded leaf greening from young pale or yellow leaf. Transcriptome analysis showed differentially expressed genes (DEGs) mainly participated in biosynthesis of amino acids, phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, sulfur metabolism, purine metabolism, and pentose and glucuronate interconversions in shading period compared with control group. The result of metabolomics indicated the total catechins level of shading group was significantly decreased than the control; however, the abundance of caffeine was markedly increased, and theanine level was nearly not influenced. Whole-genome DNA methylation analysis revealed that the global genomic DNA methylation patterns of shading period were remarkably altered compared with the control. Furthermore, differentially methylated regions (DMRs) and the DMR-related DEGs between shading and non-shading analysis indicated the DMR-related DEGs were the critical participants in biosynthesis of three major secondary metabolites. To sum up, these findings suggested that the altered levels of DNA methylation may be the main cause for biosynthesis changes of three major secondary metabolites in ‘Yujinxiang’.
2022-12-29 | GSE142753 | GEO
Project description:We explored the transcriptomic changes of synthetic Brassica allohexaploid by comparing to its parents using a high-throughput RNA-Seq method. A total of 35644409 sequence reads were generated, and 32642 genes were aligned from the data. There were 29260, 29060 and 29697 genes identified in Brassica rapa, Brassica carinata, and Brassica allohexaploid, respectively. We screened differentially expressed genes (DEGs) by a standard of two-fold or greater change in expression and false discovery rate (FDR) no more than 0.001. As a result, 7397 DEGs were detected between Brassica hexaploid and its parents. A large proportion of the 3184 DEGs between Brassica hexaploid and its paternal parent B. rapa was involved in biosynthesis of secondary metabolites, plant-pathogen interaction, photosynthesis, and circadian rhythm. Between Brassica hexaploid and its maternal parent B. carinata, 2233 DEGs were screened. A lot of them had functions of plant-pathogen interaction, plant hormone signal transduction, ribosome, limonene and pinene degradation, photosynthesis, and also biosynthesis of secondary metabolites. In addition, we found many transcription factor genes, methyltransferase and methylation genes that showed differential expression between Brassica hexaploid and its parents. Leaf mRNA profiles of Brassica rapa, Brassica carinata, and Brassica allohexaploid
2014-10-10 | E-GEOD-46299 | biostudies-arrayexpress
Project description:Tobacco, as an important cash crop and model plant, has been studied and explored in various aspects. In China, Yunyan 87 was recognized as a flue-cured tobacco variety and had been widely concerned due to its excellent product quality characteristics. The quality of tobacco products depends on the compound collection of tobacco leaves, including pigments, carbohydrates, amino acids, polyphenols and alkaloids. Present study investigated tobacco seedlings, with the assistant of the untargeted metabonomic technology and the label-free proteomic technology to analyze metabolites and proteins differences in leaf, stem, and root groups respectively. From 298 metabolites and 4993 proteins obtained, there were significant differences in both primary and secondary metabolism involved aroma precursors biosynthesis in seedling tobacco leaves, stems, and roots, such as carbohydrate metabolism, energy metabolism, and amino acid biosynthesis, and secondary metabolism phenylpropanoids, flavonoids and alkaloid biosynthesis in this study. Especially alkaloids metabolites identification results showed nornicotine, anatabine, anatalline, and myosmine, were significantly higher in tobacco roots than in leaves, and stems at seedling stage.
2022-07-12 | PXD032082 | Pride
Project description:Carotenoids have been demonstrated to be indispensable plant secondary metabolites that are involved in photosynthesis, antioxidation, and phytohormone biosynthesis. Carotenoids are likely involved in other biological functions that have yet to be discovered. In this study, we utilized genomic expression investigation to gain a deep insight into the carotenoid-related biological processes in the citrus calli overexpressing CrtB.
2014-09-23 | GSE61633 | GEO
Project description:Aflatoxins are highly toxic secondary metabolites produced mainly by Aspergillus flavus and A. parasiticus, which colonize a wide variety of food commodities especially under dry and hot conditions. We developed transgenic peanut expression four RNAi genes NsdC, Vea, Ver1 and aflR, by Agrobacterium-mediated transformation. To understand the proteome changes in 4RNAi and WT control lines, a label-free quantitative proteomics analysis was performed at 0, 30, 48 and 72 h after A. flavus inoculation using UPLC-ESI-MS/MS. Several resistance proteins in the secondary metabolic pathways related to phenylpropanoids, flavonoids, and fatty acid biosynthesis were strongly induced in the resistant genotype.
2021-09-02 | PXD028196 | JPOST Repository
Project description:397 differentially expressed proteins (78 up-regulated and 319 down-regulated) were obtained in proteome. Biosynthesis of secondary metabolites were mainly enrichment pathway of up-regulated expressed proteins.
2023-02-09 | PXD039978 | iProX
Project description:To explore the mechanisms of cotton response to this alkaline stress, we used next-generation sequencing (NGS) technology to study transcriptional changes of cotton under NaHCO3 alkaline stress. A total of 18,230 and 11,177 differentially expressed genes (DEGs) were identified in cotton roots and leaves, respectively. Gene ontology (GO) analysis indicated the enrichment of DEGs involved in various stimuli or stress responses. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs associated with plant hormone signal transduction, amino acid biosynthesis, and biosynthesis of secondary metabolites were regulated in response to the NaHCO3 stress. We further analyzed genes enriched in secondary metabolic pathways and found that secondary metabolites were regulated to eliminate the reactive oxygen species (ROS) and improve the cotton tolerance to the NaHCO3 stress. In this study, we learned that the toxic effect of NaHCO3 was more profound than that of NaOH at the same pH. Thus, Na+, HCO3- and pH had a great impact on the growth of cotton plant. The novel biological pathways and candidate genes for the cotton tolerance to NaHCO3 stress identified from the study would be useful in the genetic improvement of the alkaline tolerance in cotton.
2022-01-26 | GSE165472 | GEO