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Article|14 Jun 2017|OPEN
An eFP browser for visualizing strawberry fruit and flower transcriptomes
Charles Hawkins1,2 , Julie Caruana1 , Jiaming Li1,3 , Chris Zawora1 , Omar Darwish4 and Jun Wu3 , Nadim Alkharouf4 , Zhongchi Liu,1 ,
1Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
2Current address: Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, USA.
3Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
4Department of Computer and Information Sciences, Towson University, Towson, MD 21252, USA
*Corresponding author. E-mail: zliu@umd.edu

Horticulture Research 4,
Article number: 29 (2017)
doi: https://doi.org/10.1038/hortres.2017.29
Views: 724

Received: 16 Mar 2017
Revised: 15 May 2017
Accepted: 16 May 2017
Published online: 14 Jun 2017

Abstract

Wild strawberry Fragaria vesca 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 Rosaceae 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 Arabidopsis 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.