StCDF1 transcription factor: "The jack of all trades" and its nitrogen signalling regulation in potato [DAP-seq]
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ABSTRACT:
PROVIDER: PRJNA838617 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19226309_1.fastq.gz | Fastqsanger.gz | |||
| SRR19226309_2.fastq.gz | Fastqsanger.gz | |||
| SRR19226310_1.fastq.gz | Fastqsanger.gz | |||
| SRR19226310_2.fastq.gz | Fastqsanger.gz | |||
| SRR19226311_1.fastq.gz | Fastqsanger.gz |
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Project description:Due to the sessile nature of plants, they are under increased risk of environmental threats,aggravated by climate-change induces abiotic stress. However, plants have adapted toachieve growth development and reproduction by modulating their molecular stressresponse. Transcription factors (TFs) encoded belonging to DNA-BINDING WITH ONEFINGER (DOF) as CYCLING DOF FACTOR (CDFs) have been implicated in diverseprocesses, including nitrogen response. In potato,StCDF1TF plays a central role as a clockoutputthat regulatestuberizationand we previously demonstrated that it is also involved indrought response together with its antisense lncRNAthroughstomata regulation.Using arecently developed high-throughput DNA-affinity purification sequencing technology(DAP-Seq) we were able to identify the molecular targets of StCDF1. We further combinedDAP-Seq & RNA-Seq data from overexpressed and knockdownStCDF1transgenic plants,to specify its downstream candidate targets. We found that in addition to its canonical roleas a repressor, StCDF1 can also act as an activator of target genes involved in a range ofbiological processes, including the regulation of nitrogen metabolism. Finally, wedemonstrated that plants overexpressingStCDF1are more sensitive to lownitrogenconditions compared to the knockoutStCDF1
2024-12-18 | GSE203123 | GEO
Project description:Due to the sessile nature of plants, they are under increased risk of environmental threats,aggravated by climate-change induces abiotic stress. However, plants have adapted toachieve growth development and reproduction by modulating their molecular stressresponse. Transcription factors (TFs) encoded belonging to DNA-BINDING WITH ONEFINGER (DOF) as CYCLING DOF FACTOR (CDFs) have been implicated in diverseprocesses, including nitrogen response. In potato,StCDF1TF plays a central role as a clockoutputthat regulatestuberizationand we previously demonstrated that it is also involved indrought response together with its antisense lncRNAthroughstomata regulation.Using arecently developed high-throughput DNA-affinity purification sequencing technology(DAP-Seq) we were able to identify the molecular targets of StCDF1. We further combinedDAP-Seq & RNA-Seq data from overexpressed and knockdownStCDF1transgenic plants,to specify its downstream candidate targets. We found that in addition to its canonical roleas a repressor, StCDF1 can also act as an activator of target genes involved in a range ofbiological processes, including the regulation of nitrogen metabolism. Finally, wedemonstrated that plants overexpressingStCDF1are more sensitive to lownitrogenconditions compared to the knockoutStCDF1
2024-12-18 | GSE203114 | GEO
Project description:StCDF1 transcription factor: "The jack of all trades" and its nitrogen signalling regulation in potato
| PRJNA838611 | ENA
Project description:StCDF1 transcription factor: "The jack of all trades" and its nitrogen signalling regulation in potato [RNA-seq]
| PRJNA838597 | ENA
Project description:Nitrogen (N) can be absorbed by plants, thereby affects plant physiological activity, interferes gene expression, alters metabolite content and influences plant growth. However, the molecular mechanism underlying the potato tuberization response to nitrogen remains unclear. The plants were cultivated in the pots using N-deficient, N-Routine and N-sufficient conditions. Physiological response analysis, transcriptomics and metabolomics were performed on potato stolon exposed to Nitrogen stress. Transcriptomics analysis revealed that 2756 differentially expressed genes (DEGs) responded to nitrogen stress. By using metabolomics analysis, a total of 600 d differentially accumulated metabolites (DAMs) were identified. Further correlation analysis of major DEGs and DAMs showed that 9 key DEGs were involved in alpha-linolenic acid metabolism, 16 key DEGs in starch and sucrose metabolism, 7 key DEGs in nitrogen metabolism, and 16 key DEGs in ABC transporters. Nitrogen deficiency significantly up-regulated the contents of sucrose, GDP-glucose and L-glutamic acid, and promoted the growth of stolon by up-regulating the expression of AMY, SBE, SS, SPS, AGPS and NR-related genes. However, High nitrogen is the opposite. In addition, high nitrogen treatment up-regulated EG, SUS and GDH related genes, accumulated a large number of 9 (S) -HpOTr E, 13 (S) -HpOTr E and L-Glutamine, ultimately affected the balance between plant growth and defense. In general, our study revealed the co-expressed genes and potential pathways related to potato tuber formation under different nitrogen conditions. These comprehensive analysis data provide a better understanding of improving potato tuber traits at the molecular and metabolic levels.
2024-10-23 | GSE271112 | GEO
Project description:To screen genes related to the development of sweet potato tuberous roots, the high throughput sequencing of different stages of sweet potato tuberous roots was performed. The fibrous roots (FR; roots at 20 dap), developing tuberous roots (DR; roots at 60 dap) and mature tuberous roots (MR; roots at 120 dap) of Ipomoea batatas (L.) Taizhong 6 and MBP3 overexpressed lines were used for transcriptome analysis. Totally, we identified 5488 differentially expressed genes between different stage tuberous roots of Taizhong6 and 14312 differentially expressed genes between the tuberous roots of Taizhong6 and MBP3 overexpressed lines, by calculating the gene FPKM in each sample and conducting differential gene analysis. This study provides a foundation for the mechanism analysis of sweet potato tuberous root development.
2023-10-12 | GSE245185 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2024-12-18 | GSE203124 | GEO
Project description:Nitrogen (N) fertilization is an important abiotic factor for the growth of potato (S. tuberosum) because of its potential effects on yield. Because excess N in the soil runs off into water systems and negatively impacts the environment, studies on N use by the plant are key to decrease N-fertilizer use. Three commercial potato cultivars (Shepody, Russet-Burbank and Atlantic) were grown under two different rates of applied N-fertilizer (0 kg N ha-1 and 180 kg N ha-1) to obtain more information on the underlying gene regulation mechanisms associated with N. Plants with no added N had significantly lower concentrations of petiole nitrates, chlorophyll level indices, biomass and yield per hectare. Total mRNA samples were taken at two different time-points during the growth season and used for sequencing. The results for each cultivar and time-point were analysed separately to find differentially expressed genes. In total, thirty genes were found to be over-expressed and nine genes were found to be under-expressed in plants from all potato cultivars when they were grown with added N-fertilizer. The 1000 bp upstream flanking regions of the differentially expressed genes were analysed to find overrepresented motifs using three motif discovery algorithms (Seeder, Weeder and MEME). Nine different motifs were found, indicating potential gene regulatory mechanisms for potato under N-deficiency.
2016-06-21 | GSE75926 | GEO
Project description:The purpose of this study is to survey gene expression of potato (solanum tuberosum gilroy) in a variety of tissues and life cycle timepoints. Potato plants were grown from true seeds, planted in either soil or MS media, and grown in growth chambers. Four biological replicates each of twenty different tissue samples were collected at the appropriate timepoints. The samples were immediately frozen at -80. The tissues were then ground into a powder in liquid nitrogen, and RNA was extracted using Qiagen's QiaShredder columns and Qiagen's Rneasy MinElute Kit. The RNA was amplified using Arcturus' RiboAmp RNA Amplification Kit. 1ug of amplified RNA was used in TIGR's indirect labelleling procedure. All hybridaztions were applied to TIGR's 10kV4 potato array. Keywords: Loop design
2008-02-13 | GSE10490 | GEO
Project description:Background: A reasonable supply of nitrogen (N) fertilizer is essential for obtaining high-quality, high-level, and stable potato yields, and an improvement in the N utilization efficiency can effectively reduce N fertilizer use. It is important to use accurate, straightforward, and efficient transgenic breeding techniques for the identification of genes that can improve nitrogen use efficiency, thus enabling us to achieve the ultimate goal of breeding N-efficient potato varieties. In recent years, some of the mechanisms of miRNAs have been elucidated via the analysis of the correlation between the expression levels of potato miRNA target genes and regulated genes under conditions of stress, but the role of miRNAs in the inhibition/expression of key genes regulating N metabolism under N stress is still unclear. Our study aimed to identify the role played by specific enzymes and miRNAs in the responses of plants to N stress. Results: The roots and leaves of the N-efficient potato variety, Yanshu4 ("Y"), and N-inefficient potato variety, Atlantic ("D"), were collected at the seedling and budding stages after they were exposed to different N fertilizer treatments. The miRNAs expressed differentially under the two types of N stress and their corresponding target genes were first predicted using miRNA and degradome analysis. Then, quantitative polymerase chain reaction (qRT-PCR) was performed to verify the expression of differential miRNAs that were closely related to N metabolism. Finally, the shearing relationship between stu-miR396-5p and its target gene StNiR was determined by analyzing luciferase activity levels. The results showed that NiR activity increased significantly with an increase in the applied N levels from the seedling stage to the budding stage, and NiR responded significantly to different N treatments. miRNA sequencing enabled us to predict 48 families with conserved miRNAs that were mainly involved in N metabolism, carbon metabolism, and amino acid biosynthesis. The differences in the expression of the following miRNAs were identified via screening (high expression levels and P < 0.05): stu-miR396-5p, stu-miR408b-3p_R-1, stu-miR3627-3p, stu-miR482a-3p, stu-miR8036-3p, stu-miR482a-5p, stu-miR827-5p, stu-miR156a_L-1, stu-miR827-3p, stu-miR172b-5p, stu-miR6022-p3_7, stu-miR398a-5p, and stu-miR166c-5p_L-3. Degradome analysis showed that most miRNAs had many-to-many relationships with target genes. The main target genes involved in N metabolism were NiR, NiR1, NRT2.5, and NRT2.7. qRT-PCR analysis showed that there were significant differences in the expression levels of stu-miR396-5p, stu-miR8036-3p, and stu-miR482a-3p in the leaves and roots of the Yanshu4 and Atlantic varieties at the seedling and budding stages under conditions that involved no N and excessive N application; the expression of these miRNAs was induced in response to N stress. The correlation between the differential expression of stu-miR396-5p and its corresponding target gene NiR was further verified by determining the luciferase activity level and was found to be strongly negative. Conclusion: The activity of NiR was significantly positively correlated with N application from the seedling to the budding stage. Differential miRNAs and target genes showed a many-to-many relationship with each other. The expression of stu-miR396-5p, stu-miR482a-3p, and stu-miR8036-3p in the roots and leaves of the Yanshu4 and Atlantic varieties at the seedling and budding stages was notably different under two types of N stress. Under two types of N stress, stu-miR396-5p was down-regulated in Yanshu4 in the seedling-stage and shoot-stage roots, and up-regulated in seedling-stage roots and shoot-stage leaves; stu-miR482a-3p was up-regulated in the seedling and shoot stages. The expression of stu-miR8036-3p was up-regulated in the leaves and roots at the seedling and budding stages, and down-regulated in roots under both types of N stress. The gene expressing the key enzyme involved in N metabolism, StNiR, and the stu-miR396-5p luciferase assay reporter gene had a strong regulatory relationship with each other. This study provides candidate miRNAs related to nitrogen metabolism and highlights that differential miRNAs play a key role in nitrogen stress in potato, providing insights for future research on miRNAs and their target genes in nitrogen metabolic pathways and breeding nitrogen-efficient potatoes.
2022-10-12 | GSE199457 | GEO