De novo sequencing and comparative analysis of the Vaccinium corymbosum L. transcriptome to discover putative genes related to antioxidants

Blueberry, Vaccinium corymbosum L., is an economically and nutritionally important crop of the Vaccinium family. However, there are not sufficient tissue-specific transcriptome and genomic data in public databases for understanding of the molecular mechanism underlying pigment accumulation. Thus, high throughput Illumina second generation sequencing is needed to generate enormous transcript sequences from blueberry skin and pulp for gene discovery and molecular marker development. In this study, transcriptome analyses were used to identify different gene expressions from skin and pulp. In total, more than 64 million sequencing reads corresponding to 4.8 Gb total nucleotides were generated using Illumina paired end sequencing technology. De novo assembly yielded 34,464 unique sequences with an average length of 735 bp. These unique sequences were further functionally annotated by comparing their sequences to known protein based on BLASTX with a cut-off E-value above 10-5. A total of 25,376 (73.63%) genes were identified from National Center for Biotechnology Information non-redundant databases. Out of these annotated unigenes, 18,201 (52.8%), 12,547 (36.4%), 9,175 (26.6%) and 6,585 (19.1%) unigenes were assigned to Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), (COG) and Gene Ontology (GO), respectively. This study generated a large set of blueberry transcript sequences, which can be used to discover mechanisms of tissue specific functions and secondary metabolism and will also make it possible to construct high density microarrays for further characterization of gene expression profiles during these processes. Additionally, these results also suggested that transcriptome analysis based on Illumina paired-end sequencing is a powerful tool for functional genomics analysis, molecular marker development and blueberry breeding, especially for non-model plant organisms.