Ontology highlight
ABSTRACT:
PROVIDER: PRJNA562088 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10020074_1.fastq.gz | Fastqsanger.gz | |||
| SRR10020074_2.fastq.gz | Fastqsanger.gz | |||
| SRR10020075_1.fastq.gz | Fastqsanger.gz | |||
| SRR10020075_2.fastq.gz | Fastqsanger.gz | |||
| SRR10020076_1.fastq.gz | Fastqsanger.gz |
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Project description:We report the high-throughput profiling of miRNAs in banana. By deep sequencing and computational and molecular analyses, we identify 113 known and 26 banana-specific miRNAs and we characterize their expression pattern under cold and heat stress. We find that 42 banana miRNAs are temperature-responsive. By degradome sequencing, we identify 60 targets for known miRNAs and half of these targets are regulated by 15 temperature-responsive miRNAs. The correlative expression patterns between several miRNAs and their target genes are further validated via qRT-PCR. Our results provide a foundation for understanding the miRNA-dependent temperature stress response in banana and the characterized correlations between miRNAs and their responses to cold or heat stress could serve as markers in the breeding programs or tools for biotechnological approaches for improving temperature stress tolerance of banana.
2018-09-18 | GSE77590 | GEO
Project description:Cold-sensitive Cavendish Banana and relatively cold-tolerant Dajiao (Musa spp.) comprise an important part of diets for millions of people around the globe. Low temperature is one of the key environment stresses which greatly affect the global banana production. However, little is known about the changes of global protein phosphorylation in Musa spp. and their regulatory roles in response to cold stress. In this study, we employed a TMT6-plex quantitative analysis to conduct a global phosphoproteome profiling between Cavendish Banana and Dajiao subject to the cold stress for 0 hour and 3 hour. A total of 679 phosphopeptides containing 772 distinct phosphorylated sites from 529 phosphoproteins were identified in Cavendish Banana, 180 phosphorylation sites (belonging to 147 phosphoproteins) were differentially changed after 3 h cold stress. While in Dajiao 241 phosphopeptides with 271 individual phosphosites from 207 phosphoproteins were confidently identified, and 83 phosphorylation sites from 63 phosphoproteins were differentially changed under 3 h cold stress. Bioinformatic analysis of protein interaction network indicated that Mitogen-activated protein kinase kinase 2 (MKK2) was located in the center of the MAPK signaling network along with 7 other members whose phosphorylated site abundances were remarkably differentiated between Cavendish Banana and Dajiao in response to cold stress. Western blotting of MKK2 protein and its T31 phosphorylated site showed the increased expression of MKK2 in the time course of cold stress, with no detectable T31 phosphorylation in Cavendish Banana. On the contrary, the decreased MKK2 expression with increased T31 phosphorylation was consistently observed in Dajiao. These results suggest that the MKK2 interaction network in Dajiao, along with other cold-specific phosphoproteins found in this study, appears to play an important role in the molecular mechanisms of Dajiao being high tolerance to cold stress. The results also provide new evidence that cellular MKK2 phosphorylation as a signaling pathway plays an important role in abiotic stress tolerance that serves as a universal plant cold tolerance mechanism. To the best of our knowledge, this is the first report of MKK2 network involved in the regulatory of the Musa spp. response to cold stress.
2017-01-24 | PXD004177 | Pride
Project description:'Systems-wide' approaches such as microarray RNA-profiling are ideally suited to the study of the complex, overlapping responses of plants to biotic and abiotic stresses. However, commercial microarrays are only available for a limited number of plant species and development costs are so substantial as to be prohibitive for most research groups. Here, we evaluate the use of cross-hybridisation to Affymetrix oligonucleotide GeneChip microarrays to profile the response of the banana (Musa sp.) leaf transcriptome to drought stress using a genomic DNA (gDNA)-based probe-selection strategy to improve the efficiency of detection of differentially expressed Musa transcripts. GeneChip analyses were performed to profile the response of the banana (Musa sp.) leaf transcriptome to drought stress using a genomic DNA (gDNA)-based probe-selection strategy to improve the efficiency of detection of differentially expressed Musa transcripts.
2009-07-04 | E-GEOD-16865 | biostudies-arrayexpress
Project description:PARE (parallel analysis of RNA ends) was performed to study the change of uncapped mRNAs before and after cold treatment in Brachypodium. Different change patterns were identified. We have provided a complete view of uncapped transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants.
2013-07-15 | GSE48234 | GEO
Project description:Stress acclimation is an effective mechanism that plants acquired for adaption to dynamic environmental conditions. After undergoing cold acclimation, plants become more tolerant to cold stress. In order to understand the mechanism of cold acclimation, we performed a systematic, comprehensive study of cold response and acclimation in Cassava (Manihot esculenta), a staple crop and major food source in the tropical regions of the world. We profiled mRNA genes and small-RNA species, using next generation sequencing, and performed an integrative analysis of the transcriptome and microRNAome of Cassava across the normal condition, a moderate cold stress at 14M-BM-0C, a harsh stress at 4M-BM-0C after cold acclimation at 14M-BM-0C, and a cold shock from 24M-BM-0C to 4M-BM-0C. Two results from the analysis were striking. First, the moderate stress and cold shock, despite a difference of 10M-BM-0C between the two, triggered comparable degrees of perturbation to the transcriptome; in contrary, further harsh stress after cold acclimation resulted in a much smaller degree of transcriptome variation. Second and more importantly, about two thirds of the up- or down-regulated genes after moderate stress reversed their expression to down- or up-regulation, respectively, under harsh stress after cold acclimation, resulting in a genome-wide rewiring of regulatory networks. MicroRNAs, which are key post-transcriptional gene regulators, were major players in this massive rewiring of genetic circuitry. Further, a function enrichment analysis of the perturbed genes revealed that cold acclimation helped the plant to develop immunity to further harsh stress by exclusively inducing genes with functions of nutrient reservoir; in contrast, many genes with functions of viral reproduction were induced by cold shock. Our study revealed, for the first time, the molecular basis of stress acclimation in plants, and shed lights on the role of microRNA gene regulation in cold response and acclimation in Euphorbia. Three organs/tissues (folded leaf, fully expanded leaf and roots) of Cassava cultivar SC124 harvested at 6h, 24h and 5d for three cold treatments of CA, CCA and CS, for gene expression profiling at the stages of initial response, secondary response, and functional adaption to cold stresses. Total RNA of each sample was isolated individually, and then pooled with an equal amount from each sample into one for profiling. As a result, four mRNA libraries and four small-RNA libraries, corresponding to the conditions of CA, CCA, CS and NC, were constructed.
2014-08-18 | E-GEOD-52176 | biostudies-arrayexpress
Project description:Leaf proteomics of two different cold tolerance winter rapeseed cultivars under cold stress
2021-04-24 | PXD023323 |
Project description:Leaf rolling and discoloration are two chilling injury symptoms that are widely adopted as indicators for evaluation of cold tolerance at the seedling stage in rice, respectively. However, their relationship has not been well investigated, in particular the mechanism on how low temperature causes leaf rolling at a genome-wide level. In this study, a cold-tolerant japonica cultivar Lijiangxintuanheigu and a cold-sensitive indica cultivar Sanhuangzhan-2 were subjected to different low temperature treatments and physiological and genome-wide gene expression analysis were conducted. Our results showed that leaf rolling happened at temperatures lower than 11℃, but discoloration appeared at moderately low temperatures, such as 13℃. Chlorophyll contents of the two cultivars significantly decreased under 13℃, but didn’t change under 11℃. Contrastly, their relative water contents and the relative electrolyte leakages decreased significantly. Genome-wide gene expression profiling of LTH revealed that the calcium signaling related genes and the genes related to ABA degradation significantly changed under 11℃. Moreover, numerous genes in DREB, MYB, bZIP, NAC, Zin finger, bHLH, WRKY gene families were differently expressed. Furthermore, many aquaporin genes, the key genes in trehalose and starch synthesis were down-regulated under 11℃. These results suggest that the two chilling injury symptoms are controlled by different mechanisms. Cold-induced leaf rolling is associated with calcium and ABA signaling pathways, and subjected to regulation of multiple transcription regulators. The suppression of aquaporin genes and reduced accumulation of soluble sugars under cold stress result in reduction of water potential in cells and consequently, leaf rolling.
2019-03-30 | GSE112547 | GEO
Project description:Sunflower is an important source of vegetable oil worlwide. A differential organ-specific sunflower ESTs was previously generated by a subtractive hybridization method, including a considerable number of abiotic stress associated sequences. The objective of this work is to analyze the sunflower gene expression of previously identified candidate genes under a comprehensive microarray analysis of the leaf transcriptoma under cold and salinity stresses, considering the impacts of these abiotic stresses on sunflower yield in many productive areas. The aimed of this work is to perform genome analysis of sunflower based on its functional regions and the characterization of the sunflower transcriptoma profiles for different organ-specific genes. Abiotic-related expressed genes were the target of this characterization through a gene expression analysis of the local EST bank (annotated according to Gene Ontology Annotation) using a cDNA organ-specific microarray chip approach. We analyzed 287 differentially expressed genes derived from leaf, stem, R1 and R4 flower developmental stages. Transcriptional analysis allowed the detection of three different groups of genes according to their expression patterns. Group 1 contained 112 up-regulated genes under abiotic stress conditions (cold or salinity), whereas Group 2 (126 genes) did not show changes in their expression levels. On the other hand, 49 genes were classified as Group 3 included were down-regulated genes under both stresses. Eighty genes exhibited a significative fold change under abiotic stress conditions, being six of them validated by qRT-PCR. Microrarray profiling of cold and NaCl-treated sunflower leaves revealed dynamic changes in transcript abundance, including transcription factors, defense/stress related proteins, and effectors of homeostasis, all of which highlight the complexity of both stress responses. This finding provides identification of many transcriptional processes occurring under abiotic stress in sunflower for genes isolated from organ-specific cDNA libraries Keywords: gene expression profile of organ-specific sunflower transcriptoma in response to NaCl and cold
2008-01-29 | GSE6201 | GEO
Project description:Banana is an important tropical fruit with high value. One main specie (cultivar Cavendish) is susceptible to low temperature, another close relative specie (Dajiao), considerably higher cold tolerance than Cavendish. Our previous global proteomics results suggested that some membrane proteins be likely involved in cold tolerance of Dajiao via antioxidation mechanism. To further investigate early cold stress response of Dajiao, we applied comparative membrane proteomics analysis for both cold-sensitive Cavendish and cold-tolerant Dajiao subjected to 10 °C for 0, 3 and 6 h.
2018-10-23 | PXD007784 | Pride