An eFP browser for visualizing strawberry fruit and flower transcriptomes

Abstract

Wild strawberry <i>Fragaria vesca</i> is emerging as an important model system for the cultivated strawberry due to its diploid genome and availability of extensive transcriptome data and a range of molecular genetic tools. Being able to better utilize these tools, especially the transcriptome data, will greatly facilitate research progress in strawberry and other <i>Rosaceae</i> fruit crops. The electronic fluorescent pictograph (eFP) software is a useful and popular tool to display transcriptome data visually, and is widely used in other model organisms including <i>Arabidopsis</i> and mouse. Here we applied eFP to display wild strawberry RNA sequencing (RNA-seq) data from 42 different tissues and stages, including various flower and fruit developmental stages. In addition, we generated eight additional RNA-seq data sets to represent tissues from ripening-stage receptacle fruit from yellow-colored and red-colored wild strawberry varieties. Differential gene expression analysis between these eight data sets provides additional information for understanding fruit-quality traits. Together, this work greatly facilitates the utility of the extensive transcriptome data for investigating strawberry flower and fruit development as well as fruit-quality traits.