Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/18/2013
Publication Date: 12/23/2013
Publication URL: http://handle.nal.usda.gov/10113/61443
Citation: Darwish, O., Slovin, J.P., Kang, C., Hollender, C., Geretz, A., Houston, S., Liu, Z., Alkharouf, N. 2013. FveGD: an online resource for diploid strawberry (fragaria vesca) genomics data. Biomed Central (BMC) Plant Biology. 13:223. Interpretive Summary: Strawberry is a popular and nutritious food enjoyed worldwide. Many plant genes are involved in growth and development of strawberry fruit. Understanding how these genes function requires the ability to store and analyze very large amounts of data. In this paper we report the development of a publically accessible easy to use database of information on genes that are turned on in strawberry fruit during early stages of fruit development. The database can be found at a website (http://bioinformatics.towson.edu/strawberry/Default.aspx) that also houses tools for searching for any specified strawberry gene and for obtaining estimates of how active that gene was in fruit tissue. This database and the tools provided at the website will be used by scientists working on strategies to improve strawberry and related crops such as peach and apple.
Technical Abstract: Fragaria vesca, a diploid strawberry species commonly known as the alpine or woodland strawberry, is a versatile experimental plant system that is an emerging model for the Rosaceae family. An ancestral F. vesca genome contributed to the genome of the octoploid dessert strawberry (F. xananassa) and the extant genome exhibits synteny with other commercially important members of the Rosaceae family such as apple and peach. To provide a molecular description of floral organ and fruit development at the resolution of specific tissues and cell types during key reproductive developmental stages, RNAs from flowers and early developmental stage fruit tissues of the inbred F. vesca line YW5AF7 were extracted and the resulting cDNA libraries sequenced using an Illumina HiSeq2000. This sequence data will enable researchers to correlate gene expression with gene function during flower and fruit development in the woodland strawberry. The Fragaria vesca Genomics Database (FveGD) is a web accessible database that contains sample description, sample statistics, gene annotation, and gene expression analysis. This information can be accessed publicly from a web-based interface at http://bioinformatics.towson.edu/strawberry/Default.aspx. The FveGD website provides user friendly search and browse capabilities for all the data stored in the database. Users are able to search for genes using a gene ID or description. Search results can be downloaded in a tabular format compatible with Microsoft excel application. Transcriptome data, genome sequence, and predicted gene models can be displayed using the genome browser. RNA-seq data and analysis stored in the FveGD database will help researchers to investigate the underlying molecular events that accompany morphological changes during development of floral and young fruit tissues and organs.