Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1291824 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We analyzed the transcriptome of A. acutangulus roots by deep RNA sequencing to dig TAs biosynthetic genes. KOG (Eukaryotic Orthologous Groups) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses identified 48 unigenes referring to the tropane, piperidine and pyridine alkaloid biosynthesis, 145 unigenes presumably involved in distribution of arginine to TAs biosynthesis, and 86 unigenes referring to the terpenoid backbone biosynthesis. Furthermore, 82 unigenes annotated as cytochrome P450 family members seemed to be involved in secondary metabolism pathways. Previously unknown TAs biosynthetic genes in A. acutangulus, which encode littorine mutase/monooxygenase (CYP80F1) and diamine oxidase (DAO), were identified by this study.
2016-07-08 | GSE62162 | GEO
Project description:Detection of presumed proteins in the indican biosynthetic pathway of Polygonum tinctorium using transcriptome analysis
| PRJDB9130 | ENA
Project description:The resistance mechanisms evolved by insects to overcome host-plant allelochemicals is a key consideration in pest management. Camphor oil (EO) and its main component (i.e D-camphor) form a specific terpenoid-defensive system in camphor trees, Cinnamomum camphora. However, an emerging insect pest, Pagiophloeus tsushimanus has recently caused serious damage to this intractable plant species, which is largely elusive. Here, we used feeding bioassays and RNA-seq to investigate the mechanism underlying the resistance of the beetle to host-specific terpenoid defenses. Firstly, a hormetic response in both larval weight and developmental time was observed in terpenoid-feeding individuals, which is a highly generalized dose-response phenomenon in toxicology whereas occurs infrequently in the context of insect-plant interactions. Then, comparative transcriptome analysis between terpenoid-feeding and control groups indicated that both CYP450s-mediated metabolic resistance and CPs-mediated cuticular resistance were jointly employed to cope with terpenoid-induced stress. In addition, a small portion of genes involved in glucose transport pathway were up-regulated at the low D-camphor dose, suggesting an extra intake of glucose used for larval growth may contribute to a hormetic response. These findings probably implied that the dual terpenoid-resistance mechanisms existing in this specialist is an essential precondition for hormetic response in larval growth, ultimately contributing to successfully colonize host camphor trees with impunity. Overall, our study will open new avenues for understanding the insect-plant coevolutionary adaptation and developing durable pest control strategies.
2021-08-21 | GSE182420 | GEO
Project description:We studied the heat-shock response in wild-type (wt) and in absence of Mip6, an RNA binding protein with roles at multiple levels of the gene expression pathway. This study include; their transcriptome (RNA-seq), metabolome (targeted NMR) and H4K12ac epigenome (ChIP-seq) using an experimental desing that ensures that the same samples are used across all omics determinations. This facilitates data analysis approaches that can leverage fully matched, longitudinal, replicated data. These data will faciliate studies of covariation patterns across multiple molecular layers controlling and responding to RNA biogenesis.
2019-11-21 | GSE135568 | GEO
Project description:Activated lymphocytes adapt their metabolism to meet the energetic and biosynthetic demands imposed by rapid growth and proliferation. Common gamma chain (c ) family cytokines are central to this process but the role of downstream STAT5 signaling, a cardinal feature of all members, remains loosely defined. Using genome-, transcriptome- and metabolome-wide analyses, we demonstrate that STAT5 is a master regulator of energy and amino acid metabolism in CD4+ ‘helper’ T cells. Mechanistically, we find that STAT5 localizes to a suite of enhancers and promoters for genes encoding essential, often rate-limiting enzymes and transporters, where it instructs transcription through p300 recruitment and epigenetic remodeling. We also find that STAT5 licenses the activity of other metabolic agents downstream of IL-2, namely the mTOR signaling pathway and the transcription factor, MYC, and present evidence for genome-wide cooperation between STAT5 and MYC in both normal and transformed T cells. Taken together, our data provide a molecular framework for transcriptional programing of T cell metabolism downstream of c cytokines and emphasize the Jak-STAT pathway in powering cellular growth and proliferation.
2022-10-03 | GSE207265 | GEO
Project description:Genome-wide DNA sequence resources are expected to enhance our understanding of the molecular basis of plant development and lead to improvements in desirable traits in horticultural crops. In this study, we sequenced 643,366 ESTs from Eustoma grandiflorum flowers using a normalised cDNA library constructed for several different flower development stages, times of day, and pollinated stamens. The sequences were assembled into 63,401 contigs and 242,212 singletons. BlastX searches for all of the contigs in the GenBank database matched 65% of the contigs to registered sequences, while 35% presented no hits. GO mapping assigned 48% of the 63,401 contigs to GO terms. Microarray analysis showed that subsets of genes were up- or downregulated as the flower developed. The downregulated genes were enriched for GO terms related to 1) oligopeptide transport, 2) response to jasmonic acid stimulus, and 3) cell wall modification, whereas the upregulated genes were enriched for GO terms involved in 1) secondary metabolism, such as the flavonoid biosynthetic process and the terpenoid biosynthetic process, and 2) epidermal cell modification. Two-condition experiment, loop-design among 4 developmental stages. Biological replicates: 4.
2012-09-01 | E-GEOD-34332 | biostudies-arrayexpress
Project description:Chinese cedar (<i>Cryptomeria fortunei</i>) is a tree species with important ornamental, medicinal, and economic value. Terpenoids extracted from the essential oil of <i>C. fortunei</i> needles have been considered valuable ingredients in the pharmaceutical and cosmetic industries. However, the possible gene regulation mechanisms that limit terpenoid biosynthesis in this genus are poorly understood. Here, we adopted integrated metabolome analysis, transcriptome, small-RNA (sRNA), and degradome sequencing to analyze the differences in terpenoid regulatory mechanisms in two different overwintering <i>C. fortunei</i> phenotypes (wild-type and an evergreen mutant). A total of 1447/6219 differentially synthesized metabolites (DSMs)/unigenes (DEGs) were detected through metabolome/transcriptome analyses, and these DSMs/DEGs were significantly enriched in flavonoid and diterpenoid biosynthesis pathways. In <i>C. fortunei</i> needles, 587 microRNAs (miRNAs), including 67 differentially expressed miRNAs (DERs), were detected. Among them, 8346 targets of 571 miRNAs were predicted using degradome data, and a 72-miRNA-target regulatory network involved in the metabolism of terpenoids and polyketides was constructed. Forty-one targets were further confirmed to be involved in terpenoid backbone and diterpenoid biosynthesis, and target analyses revealed that two miRNAs (i.e., aly-miR168a-5p and aof-miR396a) may be related to the different phenotypes and to differential regulation of diterpenoid biosynthesis. Overall, these results reveal that <i>C. fortunei</i> plants with the evergreen mutation maintain high terpenoid levels in winter through miRNA-target regulation, which provides a valuable resource for essential oil-related bioengineering research.
2022-08-12 | MTBLS3183 | MetaboLights