Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Identification of microRNAs involved in cold stress response in grapevine.

ABSTRACT: Two small RNA libraries were generated from micropropagated â??Muscat Hamburgâ?? (Vitis vinifera) plantlets under normal and low temperatures (4 Â°C). A total of 163 known miRNAs and 299 putative novel miRNAs were detected from two small RNA libraries by Solexa sequencing. Forty-four cold-inducible miRNAs were identified through differentially expressed miRNAs (DEMs) analysis; among which, 13 belonged to upregulated DEMs while 31 belonged downregulated DEMs. This study indicated that a diverse set of miRNAs in V. vinifera are cold-inducible and may play an important role in cold stress response. Examination of small RNA populations in grapevine under cold treatment and none cold treatment.

ORGANISM(S): Vitis vinifera

SUBMITTER: Xiaoming Sun

PROVIDER: E-GEOD-68970 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Identification of cold-inducible microRNAs in grapevine.

Sun Xiaoming X Fan Gaotao G Su Lingye L Wang Wanjun W Liang Zhenchang Z Li Shaohua S Xin Haiping H

Frontiers in plant science 20150804

Low temperature is one of the most important environmental factors that limits the geographical distribution and productivity of grapevine. However, the molecular mechanisms on how grapevine responds to cold stress remains to be elucidated. MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that play an essential role during plant development and stress responses. Although miRNAs and their targets have been identified in several Vitis species, their participation during cold accu ...[more]

PMID: 26300896

Similar Datasets

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived flower development transcriptome profiling (RNA-seq) of two subspecies Methods: Flower mRNA profiles of wild-type (WT) four developmental stages and the same stages of Vitis vinifera subp vinifera were generated by deep sequencing using Illumina. Initial quality assessment was based on data passing the Illumina Chastity filtering. Subsequently, reads containing adapters and/or PhiX control signal were removed using an in-house filtering protocol. The second quality assessment was based on the remaining reads using the FASTQC quality control tool version 0.10.0. qRT–PCR validation was performed using EvaGreen assays. Results: Using an optimized data analysis workflow, we mapped about 13 to 19 million sequence reads per Vitis sample, 50 bp in length equivalent to 1.5 Gb of total sequence data by each sample. The exception was male stage G (M_G) were only 7 to 8 million sequence reads were obtained. Five genes (VvTFL1, VvLFY, VvAP1, Vv AP3, VvPI), related to flowering development, were used to validate RNA-Seq data and to test for data reproducibility through qRT–PCR. The coefficient of correlation (r) obtained between the log2 of RPKM (RNA-Seq) versus log2 of mRNA average number (RT-qPCR), varied from ≈ 0.97 (VvTLF) to ≈ 0.73 (VvPI) indicating a good correlation between both techniques and thus validating our RNA-Seq results. Conclusions: Our study represents the first detailed transcriptome analysis of four Vitis flower developmental stages, with the same individual, in three genders, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and accurate quantitative and qualitative evaluation of mRNA contentper developmental stage. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Flowering mRNA profiles of four developmental stages of Vitis wild type (WT) and the domesticated Vitis were generated by deep sequencing using Illumina HiSeq 2500.

Project description:Grape powdery mildew (PM), caused by the biotrophic ascomycete Erysiphe necator, is a devastating fungal disease that affects most Vitis vinifera cultivars. We have previously identified a panel of V. vinifera accessions from Central Asia with partial resistance to PM that possess a Ren1-like local haplotype. In this study we show that in addition to the typical Ren1-associated late post-penetration resistance, these accessions display a range of different levels of disease development suggesting that alternative alleles or additional genes contribute to determining the outcome of the interaction with the pathogen. To identify potential Ren1-dependent transcriptional responses and functions associated with the different levels of resistance, we sequenced and analyzed the transcriptomes of these Central Asian accessions at two time-points of PM infection. Transcriptomes were compared to identify constitutive differences and PM-inducible responses that may underlie their disease resistant phenotype. Responses to E. necator in all resistant accessions were characterized by an early up-regulation of 13 genes, most encoding putative defense functions, and a late down-regulation of 32 genes, enriched in transcriptional regulators and protein kinases. Potential Ren1-dependent responses included a hotspot of co-regulated genes on chromosome 18. We also identified 81 genes whose expression levels and dynamics correlated with the phenotypic differences between the most resistant accessions ?Karadzhandahal?, DVIT3351.27, and O34-16 and the other genotypes. This study provides a first exploration of the functions associated with varying levels of partial resistance to PM in V. vinifera accessions that can be exploited as sources of genetic resistance in grape breeding programs. Eight varieties (7 resistant to powdery mildew, 2 of which are V. vinifera spp. sylvestris, 5 of which are V. vinifera spp. sativa) are infected with powdery mildew (E. necator) at two timepoints (1 dpi and 5 dpi) with three replicates for each timepoint for each condition (uninfected vs. infected), for a total of 96 samples

Project description:Noble rot results from atypical infections of ripe grape berries by Botrytis cinerea. Unlike bunch rot, noble rot promotes favorable changes in grape berries and accumulation of secondary metabolites that enhance wine grape quality. Noble rot-infected berries of SÃ©millon, a white-skinned variety, were collected over three years from a commercial vineyard at the same time fruit were harvested for botrytized wine production. Transcriptomic and metabolomic data were integrated to identify pathways associated with distinct stages of noble rot. Botrytis induced the expression of known key regulators of pathways in secondary metabolism associated with berry ripening. The activation by Botrytis during noble rot of metabolic pathways associated with berry ripening was further supported by comparisons with transcriptomes of red-skinned varieties at vÃ©raison. A prominent and common outcome of noble rot and berry ripening was the enhancement of the phenylpropanoid metabolism. Induced synthesis of stilbenes, flavonoids, and anthocyanins was supported by both transcriptional and metabolite analyses. Enzyme assays and targeted gene expression analyses of samples from the three distinct years confirmed that the activation of central and peripheral phenylpropanoid pathways is a consistent hallmark of noble rot. Finally, we show that the impact of noble rot on grape metabolism is still detectable in botrytized wines. These results demonstrate that despite the late stage of terminal senescence of a plant organ, a biotic stress can cause a major reprogramming of plant metabolism leading, in case of noble rot, to the synthesis of important metabolites for grape berry flavor and aroma. The experimental design consists of 4 treatments, berries at 3 distinct stages of noble rot and berries without apparent symptoms of infection. From each treatment a total of 4 biological replicates were sequenced with RNAseq, each replicate corresponded to independent pools of 10-15 berries harvested from adjacent grapevines.

Dataset Information

Identification of microRNAs involved in cold stress response in grapevine.

Publications

Identification of cold-inducible microRNAs in grapevine.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure