Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1243466 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32919952_1.fastq.gz | Fastqsanger.gz | |||
| SRR32919952_2.fastq.gz | Fastqsanger.gz | |||
| SRR32919953_1.fastq.gz | Fastqsanger.gz | |||
| SRR32919953_2.fastq.gz | Fastqsanger.gz | |||
| SRR32919954_1.fastq.gz | Fastqsanger.gz |
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Project description:Nitrogen is the most important mineral nutrient of plant. As a worldwide and economically important vegetable, cucumber (Cucumis sativus L.) has a strong nitrogen-dependence. We took whole transcriptome sequencing approach to compare the gene expression profiles of cucumber leaves and roots grown under sufficient or insufficient nitrate supply. Analysis of the transcriptome data revealed that the root and leaf adapt different response mechanisms to long-term nitrogen deficiency. Photosynthesis and carbohydrate biosynthetic process were pronouncedly and specifically reduced in leaf, while the ion transport function, cell wall and phosphorus-deficiency response function seem systematically down-regulated in root. Genes in nitrogen uptake and assimilation are decreased in root, but some are increased in leaf under nitrogen deficiency. Several lines of evidence suggest that the altered gene expression networks support the basic cucumber growth and development likely through successful nitrogen remobilization involving in the induced expression of genes in ABA and ethylene pathways.
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Project description:We used RNA-Seq to query the Chlamydomonas reinhardtii transcriptome for regulation by CO2 concentration and by the transcription regulator CIA5(CCM1). Both CO2 concentration and CIA5 are known to play roles in induction of an essential CO2-concentrating mechanism (CCM), but the degree of interaction and the extent of global regulation beyond the CCM were not previously understood. We compared the transcriptome of a wild type strain vs. a cia5 strain under 3 CO2 supply conditions: high CO2 (H-CO2; 5%); low CO2 (L-CO2; 0.03 to 0.05%); and very-low CO2 (VL-CO2; <0.02%). Our goals were to: 1) reveal candidate genes that, through changes in their expression, distinguish multiple acclimation states induced by H-CO2, L-CO2, and VL-CO2; 2) reveal genes regulated directly or indirectly by CIA5; and 3) reveal genes responding to the interaction between CIA5 and changes in CO2 concentration. Our results revealed a small group of genes as encoding putative Ci transporters based on their expression patterns. The results also showed a massive and much broader impact on global gene regulation by CIA5/CCM1, which directly or indirectly affected 15% of the Chlamydomonas genome. The transcriptomes under L-CO2 and VL-CO2 conditions were not significantly different, suggesting that these two acclimation states must be controlled by mechanisms operating beyond transcript abundance. Both 137c wild type (cc125) and cia5 mutant were induced for 4 hours induction under H-CO2 (5%), L-CO2 (300~500 ppm), and VL-CO2 (100~200 ppm) conditions. 2 biological replicates were done for each strain -CO2 combination.
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