Solanum tuberosum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA185133 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR643260.fastq.gz | Fastqsanger.gz | |||
| SRR643261.fastq.gz | Fastqsanger.gz | |||
| SRR643262.fastq.gz | Fastqsanger.gz | |||
| SRR643263.fastq.gz | Fastqsanger.gz |
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Project description:Two small RNA libraries and 2 degradome libraries were constructed from potato tubers stored at room temperature or exposed to cold stress for deep sequencing. Through small RNA sequencing, 53 known miRNAs and 59 novel miRNAs were identified. Seventy genes were identified as miRNA targets by degradome sequencing. Small RNA sequencing and degradome sequencing of control and cold treated Solanum tuberosum tubers
2015-12-24 | E-GEOD-43237 | biostudies-arrayexpress
Project description:Two small RNA libraries and 2 degradome libraries were constructed from potato tubers stored at room temperature or exposed to cold stress for deep sequencing. Through small RNA sequencing, 53 known miRNAs and 59 novel miRNAs were identified. Seventy genes were identified as miRNA targets by degradome sequencing.
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Project description:Light is a major environmental factor that affects metabolic pathways and stimulates the production of secondary metabolites in potato. However, adaptive changes in potato metabolic pathways and physiological functions triggered by light are partly explained by gene expression changes. Regulation of secondary metabolic pathways in potato has been extensively studied at transcriptional level, but little is known about the mechanisms of post-transcriptional regulation by miRNAs. To identify light-responsive miRNAs/mRNAs and construct putative metabolism pathways regulated by the miRNA-mRNA pairs, an integrated omics (sRNAome and transcriptome) analysis was performed to potato under light stimulus. A total of 31 and 48 miRNAs were identified to be differentially expressed in the leaves and tubers, respectively. Among the DEGs, 1353 genes in the leaves and 1841 genes in the tubers were upregulated, while 1595 genes in the leaves and 897 genes in the tubers were downregulated by light. Mapman enrichment analyses showed that genes related to MVA pathway, alkaloids-like, phenlypropanoids, flavonoids, and carotenoids metabolism were significantly upregulated, while genes associated with major CHO metabolism were repressed in the leaves and tubers. Integrated miRNA and mRNA profiles revealed that light-responsive miRNAs are important regulators in alkaloids metabolism, UMP-salvage, lipid biosynthesis, and cellulose catabolism. Moreover, several miRNAs may participate in glycoalkaloids metabolism via JA signaling pathway, UDP-glucose biosynthesis and hydroxylation reaction. This study provides a global view of transcriptome response in potato response to light, our results suggest that miRNAs might play important roles in secondary metabolic pathways, especially in glycoalkaloid biosynthesis. The findings will enlighten us on the genetic regulation of secondary metabolite pathways and pave the way for future application of genetically engineered potato.
2016-09-28 | GSE79985 | GEO
Project description:Light is a major environmental factor that affects metabolic pathways and stimulates the production of secondary metabolites in potato. However, adaptive changes in potato metabolic pathways and physiological functions triggered by light are partly explained by gene expression changes. Regulation of secondary metabolic pathways in potato has been extensively studied at transcriptional level, but little is known about the mechanisms of post-transcriptional regulation by miRNAs. To identify light-responsive miRNAs/mRNAs and construct putative metabolism pathways regulated by the miRNA-mRNA pairs, an integrated omics (sRNAome and transcriptome) analysis was performed to potato under light stimulus. A total of 31 and 48 miRNAs were identified to be differentially expressed in the leaves and tubers, respectively. Among the DEGs, 1353 genes in the leaves and 1841 genes in the tubers were upregulated, while 1595 genes in the leaves and 897 genes in the tubers were downregulated by light. Mapman enrichment analyses showed that genes related to MVA pathway, alkaloids-like, phenlypropanoids, flavonoids, and carotenoids metabolism were significantly upregulated, while genes associated with major CHO metabolism were repressed in the leaves and tubers. Integrated miRNA and mRNA profiles revealed that light-responsive miRNAs are important regulators in alkaloids metabolism, UMP-salvage, lipid biosynthesis, and cellulose catabolism. Moreover, several miRNAs may participate in glycoalkaloids metabolism via JA signaling pathway, UDP-glucose biosynthesis and hydroxylation reaction. This study provides a global view of transcriptome response in potato response to light, our results suggest that miRNAs might play important roles in secondary metabolic pathways, especially in glycoalkaloid biosynthesis. The findings will enlighten us on the genetic regulation of secondary metabolite pathways and pave the way for future application of genetically engineered potato.
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Project description:St (common potato) is a freezing sensitive species unable to cold acclimate. The close wild relative Sc is freezing tolerant and able to cold acclimate. Here we compare the cold transcriptome of these two species with different levels of freezing tolerance. We also identify the putative CBF regulons by comparing the transcriptomes of wild type plants with that of 35S::AtCBF3 transgenic lines in both species.
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Project description:Samples from dormant and sprouting bud tissue from potato tubers were taken to enable global transcriptome analysis of active meristematic tissue. Data was used in a co-expression analysis using microarray data of different experimental backgrounds.
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