ena-STUDY-UOR-31-10-2013-14:19:11:051-43
Global transcriptome analysis and identification of differentially expressed genes after infection of the diploid strawberry Fragaria vesca with powdery mildew pathogen(Podosphaera aphanis)using Illumina HiSeq2000 platform
Powdery mildew is an important disease of crop plants. In strawberry, the disease is caused by the obligate biotrophic fungus Podosphaera aphanis (syn: Sphaerotheca macularis f. sp. Fragariae) and causes significant economic loss in the cultivated strawberry.To investigate the molecular mechanism underlying strawberry-powdery mildew interaction, RNA-seq was employed to generate a large transcriptome dataset in two diploid strawberry varieties, Fragaria vesca ssp. vesca accession Hawaii 4 (HW)and Fragaria vesca f. semperflorens line “Yellow Wonder 5AF7” (YW) at 1 d and 8 d after powdery mildew infection. We identified about 999 million (92%) reads mapped to the F. vesca genome. Transcripts were identified from a total of 23,470 and 23,464 genes in HW and YW, respectively at all three stages (control, 1 dai and 8 dai). Differential gene expression analysis identified 1,567, 1,846 and 1,145 upregulated genes between control and 1 dai, control and 8 dai, and 1 dai and 8 dai, respectively in HW. Similarly, 1,336, 1,619 and 968 genes were upregulated in YW. Also 646, 1,098 and 624 downregulated genes were identified in HW, while 571, 754 and 627 genes were downregulated in YW between all three stages, respectively. The study also investigated differentially expressed genes (log2 fold change >5) between control and 1DAI in both HW and YW. A large number of genes related to secondary metabolism, signal transduction, transcriptional regulation and disease resistance were expressed predominantly either in HW or YW. These included flavonoid 3´-monooxygenase, peroxidase 15, glucan endo-1, 3-beta-glucosidase 2, receptor-like kinases, transcription factors, germin-like proteins, F-box proteins, NB-ARC and NBS-LRR proteins. This first application of RNA-seq to any pathogen interaction in strawberry provides wealth of genomic information for future studies in understanding molecular and cellular processes of the strawberry defence response to powdery mildew.
Powdery mildew is an important disease of crop plants. In strawberry, the disease is caused by the obligate biotrophic fungus Podosphaera aphanis (syn: Sphaerotheca macularis f. sp. Fragariae) and causes significant economic loss in the cultivated strawberry.To investigate the molecular mechanism underlying strawberry-powdery mildew interaction, RNA-seq was employed to generate a large transcriptome dataset in two diploid strawberry varieties, Fragaria vesca ssp. vesca accession Hawaii 4 (HW)and Fragaria vesca f. semperflorens line “Yellow Wonder 5AF7” (YW) at 1 d and 8 d after powdery mildew infection. We identified about 999 million (92%) reads mapped to the F. vesca genome. Transcripts were identified from a total of 23,470 and 23,464 genes in HW and YW, respectively at all three stages (control, 1 dai and 8 dai). Differential gene expression analysis identified 1,567, 1,846 and 1,145 upregulated genes between control and 1 dai, control and 8 dai, and 1 dai and 8 dai, respectively in HW. Similarly, 1,336, 1,619 and 968 genes were upregulated in YW. Also 646, 1,098 and 624 downregulated genes were identified in HW, while 571, 754 and 627 genes were downregulated in YW between all three stages, respectively. The study also investigated differentially expressed genes (log2 fold change >5) between control and 1DAI in both HW and YW. A large number of genes related to secondary metabolism, signal transduction, transcriptional regulation and disease resistance were expressed predominantly either in HW or YW. These included flavonoid 3´-monooxygenase, peroxidase 15, glucan endo-1, 3-beta-glucosidase 2, receptor-like kinases, transcription factors, germin-like proteins, F-box proteins, NB-ARC and NBS-LRR proteins. This first application of RNA-seq to any pathogen interaction in strawberry provides wealth of genomic information for future studies in understanding molecular and cellular processes of the strawberry defence response to powdery mildew.