RNA-Seq Analysis of Blueberry Fruit Identifies Candidate Genes Involved in Ripening and Secondary Metabolism

Blueberries contain high amount of phenolic compounds, including anthocyanins, flavonols, procyanidins and other secondary metabolites, resulting in high antioxidant activity that provides health benefits. These compounds in fruit could potentially reduce the incidence or severity of chronic diseases, such as cardiovascular disease and Alzheimer’s disease. Molecular networks governing production of these compounds have been poorly understood, mainly due to lack of full complement set of genes.  Here, we aim to identify all the genes that are expressed in berries that could help in identifying the pathways responsible for synthesis of health-protective compounds and support development of new varieties with enhanced health-protective properties.

To characterize the expressed gene repetoire of blueberry, approximately, 800 million reads were generated using a combination of Illumina and 454 cDNA sequencing (RNA-seq) from Vaccinium corymbosum cv O’Neal, an early-ripening variety of southern highbush blueberry. Reads were aligned onto a draft assembly of the blueberry genome and used construct gene and transcript models. To supplement these, ab initio gene prediction programs were used to identify genes not represented in the RNA-Seq data. A filtering procedure was applied to eliminate redundant annotations, leaving 63,840 genes and 70,581 transcripts. To identify the pathways differentially expressed during the fruit ripening, we used the PlantCyc database of metabolic enzymes to identify enzymes in blueberry. We then used these annotations to construct the blueberry metabolic network database (VCcyc) using Pathologic software from Pathway Tools. Putative enzymes representing more than 450 pathways were identified, including some not previously characterized in blueberry. To enable exploration and visualization of results, data were made available in a new release of Integrated Genome Browser (IGB8), which is freely available from bioviz.org.