Ontology highlight
ABSTRACT:
PROVIDER: PRJNA646396 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12225465_1.fastq.gz | Fastqsanger.gz | |||
| SRR12225465_2.fastq.gz | Fastqsanger.gz |
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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.
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Project description:Plasmopara viticola (Berk. and Curt.) Berl. and de Toni is the agent of the destructive disease known as grapevine downy mildew, for the control of which intensive fungicide treatments are required. Natural sources of resistance are available in several wild Vitis species, which are being used in traditional breeding approaches. However, molecular switches, signals and effectors involved in resistance are poorly understood. In this paper we report a microarray analysis of early transcriptional changes associated to P. viticola infection in both susceptible Vitis vinifera and resistant Vitis riparia plants (12 and 24 h post inoculation). To provide a biological basis to the choice of time points for transcriptome analyses, we performed microscopic examinations of infected tissues at 12, 24, 48 and 96 hpi. Data suggest that resistance in V. riparia is mainly a post-infectional event and involves a large reprogramming of host metabolism. Transcripts of signal transduction-related genes are specifically and often strongly accumulated in response to infection. Well known defence genes also show marked transcript increases, especially pathogenesis-related proteins PR-10 and stylbene synthases, and genes related to an hypersensitive reaction. On the other hand, V. vinifera mounts a much weaker transcriptional response, involving mainly defence genes, not effective enough in preventing pathogen infection. Leaves from one resistant (V. riparia cv. Gloire de Montpellier) and one susceptible (V.vinifera cv. Pinot Noir) grapevine cultivars grown in vitro were infected with the oomycete Plasmopara viticola, and transcriptome changes were investigated at 12h and 24h after infection. Three biological replicates were considered and each hybridization was performed twice. One color labeling was performed
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