RNA-Seq Analysis and Annotation of a Draft Blueberry Genome Assembly

Highbush blueberry is an important small fruit crop in the US, Chile, New Zealand, and many other countries. Thanks to decades of breeding, blueberries can now be grown in many different locations and climates.  Understanding the genetic and molecular basis for valuable berry traits requires access to genome sequence and annotations. We used a combination of sequencing strategies to generate a draft genome assembly for blueberry. We annotated the assembly using RNA-Seq data from five stages of berry fruit development and ripening. Homology-based annotation assigned potential functions to more than 60% of gene models. RNA-Seq expression profiling showed that blueberry growth, maturation, and ripening involve dynamic gene expression changes, including coordinated up- and down-regulation of metabolic pathway enzymes and transcriptional regulators. Analysis of RNA-seq alignments identified developmentally regulated alternative splicing, promoter use, and 3′ end formation. Data are available for visualization in Integrated Genome Browser via an IGB Quickload site located at http://www.igbquickload.org/blueberry/.  In this talk, we'll describe these resources and highlight major results obtained from genome annotation and RNA-Seq analysis of berry fruit.