Solanum tuberosum
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ABSTRACT:
PROVIDER: PRJNA13297 | ENA |
REPOSITORIES: ENA
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Project description:As part of a wider project to assess the impact of ultrasound on in vitro plant growth, this paper aimed to determine whether the application of piezoelectric ultrasound (PE-US) would induce changes to the transcriptome of in vitro potato (Solanum tuberosum L.). After exposing explants (single-node segments with a single leaf) to PE-US (35 kHz; 70 W) for 20 min, the effect of this stressor was determined at 0 h, 24 h, 48 h, 1 w and 4 w to assess the possible immediate and residual effects of PE-US on the potato transcriptome.
2020-03-03 | GSE135294 | GEO
Project description:Phloem localization of plant viruses is advantageous for acquisition by sap-sucking vectors but hampers host-virus protein interaction studies. In this study, Potato leafroll virus (PLRV)-host protein complexes were isolated from systemically infected potato, a natural host of the virus. Comparing two different co-immunoprecipitation support matrices coupled to mass spectrometry, we identified 44 potato proteins and one viral protein (P1) specifically associated with virus isolated from infected phloem. An additional 142 proteins interact in complex with virus at varying degrees of confidence. Greater than 80% of these proteins were previously found to form high confidence interactions with PLRV isolated from the model host Nicotiana benthamiana. Bioinformatics revealed that these proteins are enriched for functions related to plasmodesmata, organelle membrane transport, translation and mRNA processing. Our results show that model system proteomics experiments are extremely valuable for understanding protein interactions regulating infection in recalcitrant pathogens such as phloem-limited viruses.
2016-12-14 | PXD004814 | Pride
Project description:Purpose: MicroRNAs (miRNAs) are ubiquitous components of endogenous plant transcriptome. miRNAs are small, single-stranded and ~21 nt long RNAs which regulate gene expression at the post-transcriptional level and are known to play essential roles in various aspects of plant development and growth. Previously, a number of miRNAs have been identified in potato through in silico analysis and deep sequencing approach. However, identification of miRNAs through deep sequencing approach was limited to a few tissue types and developmental stages. This study reports the identification and characterization of potato miRNAs in three different vegetative tissues and four stages of tuber development by high throughput sequencing. Results: Small RNA libraries were constructed from leaf, stem, root and four early developmental stages of tuberization and subjected to deep sequencing, followed by bioinformatics analysis. A total of 89 conserved miRNAs (belonging to 33 families), 147 potato-specific miRNAs (with star sequence) and 112 candidate potato-specific miRNAs (without star sequence) were identified. The digital expression profiling based on TPM (Transcripts Per Million) and qRT-PCR analysis of conserved and potato-specific miRNAs revealed that some of the miRNAs showed tissue specific expression (leaf, stem and root) while a few demonstrated tuberization stage-specific expressions. Targets were predicted for identified conserved and potato-specific miRNAs, and predicted targets of four conserved miRNAs, miR160, miR164, miR172 and miR171, which are ARF16 (Auxin Response Factor 16), NAM (NO APICAL MERISTEM), RAP1 (Relative to APETALA2 1) and HAIRY MERISTEM (HAM) respectively, were experimentally validated using 5′RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). Gene ontology (GO) analysis for potato-specific miRNAs was also performed to predict their potential biological functions. Conclusions: We report a comprehensive study of potato miRNAs at genome-wide level by high-throughput sequencing and demonstrate that these miRNAs have tissue and/or developmental stage specific expression profile. Also, predicted targets of conserved miRNAs were experimentally confirmed for the first time in potato. Our findings indicate the existence of extensive and complex small RNA population in this crop and suggest their important role in pathways involved in diverse biological processes, including tuber developmental process.
2014-01-09 | GSE52599 | GEO
Project description:Potato wild relatives (Solanum section Petota) are a source of genetic diversity for improving traits in modern cultivars (S. tuberosum) to meet climate challenges. Potatoes are susceptible to multiple abiotic and biotic stresses and have undergone constant improvement through breeding programs worldwide. The allotetraploid S. acaule Bitter has been used to introgress cold tolerance into potato breeding germplasm. The cold challenged transcriptome of S. acaule was compared with that of autotetraploid S. tuberosum cv. Atlantic, and was found to have fewer differentially expressed genes than the latter. Specifically, subgenome 1 has less downregulated alleles compared to subgenome 2 and S. tuberosum.
2025-05-31 | GSE268611 | GEO
Project description:Potato (Solanum tuberosum L.), as an important food crop on the Qinghai-Tibet Plateau, is prone to low temperature and frost damage during the seedling stage, causing economic losses for farmers. In this study, transcriptome analyses were conducted on the leaves of Atlantic, KY130 and KY140 potato varieties following exposure to cold stress (CS). The genes StPAL(Soltu.Atl.09_2G005110) and StGAD(Soltu.Atl.11_3G000340), suggesting their involvement in the regulation of cold resistance in potato. “Flavonoid-related metabolism,” “lipid metabolism,” “amino acid metabolism,” “carbohydrate metabolism,” “nucleotide metabolism,” and “energy metabolism” might play an important role in the cold resistance of potato. Our results provided novel insights into the molecular mechanisms underlying cold resistance in potato.
2025-03-12 | GSE291340 | GEO
Project description:Dynamics of tolerant potato-potato virus Y interaction
| PRJNA252955 | ENA
Project description:Total RNA sequencing for potato tuberization
| PRJNA589236 | ENA