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Transcriptome analysis the genes expression in SsMYRV4-infected strain Ep-1PNA367T1 and SsMYRV4-free strain Ep-1PNA367

ABSTRACT: Transcriptome analysis the genes expression in SsMYRV4-infected strain Ep-1PNA367T1 and SsMYRV4-free strain Ep-1PNA367. the two strains were grown on a cellophane membrane overlaid onto PDA medium at 20℃ for 3 days, samples were collected for total RNA extraction. The RNA samples were sequenced and anlysized by the BGI Co., Ltd. Total clean reads of each sample above 5000000.The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks.

ORGANISM(S): Sclerotinia sclerotiorum

PROVIDER: GSE94575 | GEO | 2017/02/07

REPOSITORIES: GEO

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Project description:The Solexa/Illuminaâs digital gene expression (DGE) system was used to gain insight into the broad range of transcriptional responses during the vegetative growth, sclerotial development, myceliogenic germination, carpogenic germination, apothecium formation (stipe) and infection of Sclerotinia sclerotiorum. We obtained a sequencing depth of approximately 3.3 million clean tags per cDNA library. Tag mapping indicated that these six cDNA libraries in total represented more than 66.7% of all of the genes presented in the predicted transcript databases of the Broad Institute. Thouthands of differentially expressed genes were indentified during the various developmental stages compared to the vegetative growth stage. Our results could increase and deepen the understanding of the vegetative and reproductive development as well as the infection of S. sclerotiorum The S. sclerotiorum strain Ep-1PNA367 was grown or treated under different conditions, and samples were collected for RNA extraction for DGE analysis during the following stages: (i) Vegetative stage: activating hyphal agar discs of the Ep-1PNA367 stain were placed on a cellophane membrane overlaid onto PDA medium at 20Â°C; subsequently, the mycelia were collected at 12, 24, 36, 48 and 60 h; (ii) Sclerotial formation stage: the colonies growing on the cellophane membrane overlaid onto PDA medium were further incubated under the same conditions and then the cultures were collected at 84, 96, 108, 120 and 132 h; (iii) Early stages of infection: fresh hyphal fragments of the Ep-1PNA367 strain were overlaid onto sterilized cheese cloth, which was overlaid onto the leaves of the A. thaliana ecotype Columbia-0, followed by inoculation at 20Â°C with 100% relative humility; the cheese cloth with hyphae was then rolled up from the leaves at 9 h and 12 h; (iv) Sclerotial myceliogenic germination stage: sclerotia were surface sterilized with sodium hypochlorite and were sowed on a PDA plate at 20Â°C to induce myceliogenic germination, and when approximately 50% of sclerotia had germinated, the sclerotia were harvested; (v) Sclerotial carpogenic germination stage: sclerotia were dried at room temperature and were pretreated in a freezer (4-6Â°C) for up to one month and then were surface sterilized and sowed on wet sterilized sands in a plate at 15Â°C to induce carpogenic germination; when approximately 50% of the sclerotia germinated (stipes having only emerged from sclerotia), the sclerotia were harvested; and (vi) Early apothecial formation stage: sclerotia were allowed to grow in the same incubator, and the stipes were cut and collected immediately before apothecium formation for RNA extraction. Finally, different time-point samples from the vegetative stage, sclerotial formation stage and infection stage were pooled together respectively according to equal quantities for RNA extraction.

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Transcriptome analysis the genes expression in SsMYRV4-infected strain Ep-1PNA367T1 and SsMYRV4-free strain Ep-1PNA367

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