Bioinformatic Analysis of RNA-seq Data from Cultivated Strawberry (Fragaria x ananassa) and Experimental Validation of New Transcripts Related to Cold Tolerance
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The cultivated strawberry (Fragaria × ananassa) is an important plant consumed around the world for its flavour and nutritional value. The strawberry floral organs are very sensitive to cold stress, which often leads to economic loss. To gain insight into the transcriptome contributing to cold tolerance, a comprehensive transcriptome analysis comparing octoploid strawberry (Fragaria × ananassa) cultivars was performed. RNA-seq method was used to identify transcripts associated with freezing tolerance. By performing pairwise differential expression analysis was determined the number of differentially expressed transcripts of two cultivars ‘Jonsok’ and ‘Elsanta’ that differ in the response to low-temperature stress. Moreover, the most up- and down-regulated transcripts were selected from samples treated at 2 °C through different time points 0, 1, 5, 48, 240 h. In addition, the expression profiles of 21 transcripts associated with cold tolerance were identified. Several transcripts including dehydrin COR47-like, transcription factor ICE1, chalcone synthase, cytosolic aldolase, alcohol dehydrogenase, dehydrin Xero2, E3 ubiquitin- ligase HOS1 and cleavage stimulating factor 64-like, were validated using RT-qPCR. A high compliance was obtained between bioinformatics analysis and experimental results obtained from RT-qPCR. We assume that these transcriptome data will provide a valuable foundation for further characterization of the molecular mechanisms and potentially for analysis at the proteomic level.