BBGD454: an Online Database for Blueberry Genomic Data Transcriptome analysis of Blueberry using 454 EST sequencing

NOTE: This dataset is no longer publicly available. This database houses over 500,000 sequences that were generated and assembled into approximately 15,000 contigs, annotated and functionally mapped to Gene Ontology (GO) terms. Blueberry (Vaccinium corymbosum) is a major berry crop in the United States. Next generation sequencing methodologies, such as 454, have been demonstrated to be successful and efficient in producing a snap-shot of transcriptional activities during an organism’s developmental stage(s) or its response to biotic or abiotic stresses. Such application of this new sequencing technique allows for high-throughput, genome-wide experimental verification of known and novel transcripts. We have applied a high-throughput pyrosequencing technology (454 EST sequencing) for transcriptome profiling of blueberry during different stages of fruit development to gain an understanding of the genes that are up or down regulated during this process. We have also sequenced flower buds at four different stages of cold acclimation to gain a better understanding of the genes and biochemical pathways that are up- or down-regulated during cold acclimation, since extreme low temperatures are known to reduce crop yield and cause major losses to US farmers. We have also sequenced a leaf sample to compare its transcriptome profile with that of bud and fruit samples. Over 500,000 sequences were generated and assembled into approximately 15,000 contigs and were annotated and functionally mapped to Gene Ontology (GO) terms. A database was developed to house these sequences and their annotations. A web based interface was also developed to allow collaborators to search\browse the data and aid in the analysis and interpretation of the data. The availability of these sequences will allow for future advances, such as the development of a blueberry microarray to study gene expression, and will aid in the blueberry genome sequencing effort that is underway. This work was supported by grant 2008-51180-04861 from the USDA - Cooperative State Research, Education, and Extension Service (CSREES) Specialty Crop Research Initiative program.