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Elucidating cold acclimation pathway in blueberry by transcriptome profiling

Jose V. Die, Lisa J. Rowland
Environmental and experimental botany 2014 v.106 pp. 87-98
acclimation, assays, blueberries, buds, cDNA libraries, carbohydrate metabolism, classification, cold, cold tolerance, complementary DNA, cost effectiveness, data collection, databases, gene expression, gene expression regulation, genes, lipid metabolism, prediction, quantitative polymerase chain reaction, sequence analysis, transcription factors, transcriptome, transcriptomics, zinc, zinc finger motif
A fundamental goal of cold acclimation research is to understand the mechanisms responsible for the increase in freezing tolerance in response to environmental cues. Changes in gene expression underlie some of the biochemical and physiological changes that occur during cold acclimation. Detailed and comprehensive transcriptome annotation can be considered a prerequisite for effective analysis and a fast and cost-effective way to rapidly obtain information in the context of a given physiological condition. By computational predictions and manual curation, we have annotated 454 sequence assemblies from two blueberry cDNA libraries that represent flower buds in the first and second stages of cold acclimation. Gene ontology functional classification terms were retrieved for 4343 (80.0%) sequences. GO annotation files compatible with a commonly used annotation tool have been generated and are publicly available. By mining the dataset further, it was possible to associate presence of certain transcripts related to carbohydrate metabolism and lipid metabolism with different stages of cold acclimation. This was concomitant with differential presence of Zn finger functional domains and C3H-family transcription factors. The expression of a few selected genes was validated by quantitative real-time PCR assay. Results demonstrate that our transcriptome database is a rich resource for mining cold acclimation-responsive genes.