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Saffron Transcriptome and Gene Expression

ABSTRACT: In this study, we aim to present a global transcriptome analysis of medicinal/spice plant, Crocus sativus. We generated about 206 million high-quality reads from five tissues (corm, leaf, Tepal, stamen and stigma) using Illumina platform. We performed an optimized de novo assembly of the reads and estimated transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses among tissue samples.

ORGANISM(S): Crocus sativus

PROVIDER: GSE65103 | GEO | 2016/03/04

SECONDARY ACCESSION(S): PRJNA273002

REPOSITORIES: GEO

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Dynamic transcriptomic and metabolic profiling reveal synthetic characters and regulators of apocarotenoids biosynthesis in Crocus sativus

Project description:Background: Crocus sativus L. belongs to the Iridaceae family and its dried stigma, called saffron, is one of the world’s most expensive spice. C. sativus is also a famous medicinal plant on account of producing significant pharmaceutical apocarotenoids like crocins, crocetin, picrocrocin and safranal. These metabolites have been reported to play important pharmacological efficiency towards many diseases. However, the regulatory mechanism of saffron apocarotenoids biosynthesis and stigma specific accumulation remains poorly understood. Results: In this work, we performed deep transcriptomic sequencing and dynamic metabolomic profiling of different developmental stage stigmas, and firstly integrated the dynamic changes of apocarotenoids with dynamic transcriptomic data. As a result, a co-expression network was constructed, and 41 pathway genes, 5 TF genes were identified as hub genes probably participating in apocarotenoid biosynthesis, validated by qRT-PCR. The reliability of these results was validated by previous research of several genes, which were also screened out by the co-expression network. Conclusions: This work provides novel insights into the mechanism by which the apocarotenoids is synthesized and regulated. Such gene-to-apocarotenoid landscapes associated with different developmental stigma are fundamental of deeply understanding the biosynthesis and metabolic engineering of saffron apocarotenoids in the C. sativus and other plant.

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Catharanthus Transcriptome and Gene Expression

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SPATULA and ALCATRAZ confer fruit cavity and female sterility via mediating transmitting tract development in cucumber

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Catharanthus Transcriptome and Gene Expression

Project description:In this study, we aim to present a global transcriptome analysis of medicinal plant, Catharanthus roseus. We generated about 343 million high-quality reads from three tissues (leaf, root and flower) using Illumina platform. We performed an optimized de novo assembly of the reads and estimated transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses among tissue samples. We collected different tissue samples from the mature plants. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequence data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were used for de novo assembly optimization. The reads were further mapped to the Catharanthus transcripts via CLC Genomics Workbench and differential gene expression analysis was performed using DESeq software.

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2008-06-12 | E-GEOD-3056 | biostudies-arrayexpress

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Inhibition of VCAM-1 expression by CORM-3: the role of the ubiquitin proteasome system, p38 and mitochondrial respiration

Project description:Carbon monoxide (CO) abrogates TNF-alpha mediated inflammatory responses in endothelial cells, yet, the underlying mechanism hereof is still elusive. We sought to explore potential mechanisms by which CO down-regulates VCAM-1 expression on TNF-alpha stimulated human umbilical vein endothelial cells (HUVEC). By genome-wide gene expression profiling and pathway analysis we studied the relevance of particular pathways for the anti-inflammatory effect of CO. In CO-releasing molecules-3 (CORM-3) stimulated HUVEC, significant changes in gene expression were found for genes implicated in the proteasome and porphyrine pathways. Although proteasome activities were increased by CORM-3, proteasome inhibitors did not abolish CORM-3‘s effect. Likewise, HO-1 inhibitors did not abrogate the ability of CORM-3 to down-regulate VCAM-1 expression. MAPK p38 was inhibited by CORM-3. Accordingly, VCAM-1 expression was down-regulated by the p38 inhibitor SB203580. Down-regulation of VCAM-1 by CORM-3 only occurred at concentrations that partly inhibit ATP production. Sodium azide and oligomycin paralleled the effect of CORM-3 in this regard. In conclusion, down-regulation of VCAM-1 by CORM-3 seems to be mediated via inhibition of p38 and mitochondrial respiration. Although CORM-3 up-regulates several genes in the ubiquitin proteasome sytem (UPS) or porphyrin pathway, there is no evidence that these changes are involved in the anti-inflammatory properties of CORM-3.

2011-07-11 | GSE22175 | GEO

Gene expression analysis in stigma during compatible and in-compatible pollination reactions in Lolium perenne

Project description:The expression analysis had two goals: (1) look at relative transcription within mature pollen grains (2) compare expression in the stigma during pollination with either compatible or in-compatible pollen. Two pairwise comparisons, (i) unpollinated stigma vs. stigma pollinated with compatible pollen, and (ii) unpollinated stigma vs stigma pollinated with incompatible pollen. The genotype where stigma samples were harvested from is F1-30, and this is also the pollen source during an incompatible pollination reaction. The compatible pollen source is the variety Foxtrot (heterogeneous populations).

2015-10-26 | E-MTAB-3760 | biostudies-arrayexpress

Global gene expression profiling and antibiotic susceptibility after repeated exposure to the carbon monoxide-releasing molecule-2 (CORM-2) in multidrug-resistant ESBL-producing uropathogenic Escherichia coli

Project description:Treatment of urinary tract infections is today a challenge due to the increasing prevalence of multidrug-resistant ESBL-producing uropathogenic Escherichia coli (UPEC). There is an urgent need for new treatment strategies for multidrug-resistant UPEC and preferably with targets that have low potential for development of resistance. Carbon monoxide-releasing molecules (CORMs) are novel and potent antibacterial agents. The present study examines the transcriptomic targets of CORM-2 in a multidrug-resistant ESBL-producing UPEC isolate (ESBL7) in response to a single exposure to CORM-2 and after repeated exposure to CORM-2. The bacterial viability and minimal inhibitory concentration (MIC) were also examined after repeated exposure to CORM-2. Microarray analysis revealed that a wide range of processes were affected by CORM-2, including a general trend of down-regulation in energy metabolism and biosynthesis pathways and up-regulation of the SOS response and DNA repair. Several genes involved in virulence (ibpB), antibiotic resistance (marAB, mdtABC) and biofilm formation (bhsA, yfgF) were up-regulated, while some genes involved in virulence (kpsC, fepCEG, entABE), antibiotic resistance (evgA) and biofilm formation (artIP) were down-regulated. Repeated exposure to CORM-2 did not alter the gene expression patterns, the growth inhibitory response to CORM-2 or the MIC values for CORM-2, cefotaxime, ciprofloxacin and trimethoprim.

2016-10-06 | GSE87627 | GEO

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