title: SGR: an online genomic resource for the woodland strawberry.
abstract: BACKGROUND
  Fragaria vesca, a diploid strawberry species commonly known as the alpine or woodland strawberry, is a versatile experimental plant system and an emerging model for the Rosaceae family. An ancestral F. vesca genome contributed to the genome of the octoploid dessert strawberry (F. ×ananassa), 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, 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. To enable easy access as well as mining of this two-dimensional (stage and tissue) transcriptome dataset, a web-based database, the Strawberry Genomic Resource (SGR), was developed.
  
  
  METHODS
  SGR 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 SGR 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 or obtain differentially expressed genes by entering different comparison parameters. Search results can be downloaded in a tabular format compatible with Microsoft excel application. Aligned reads to individual genes and exon/intron structures are displayed using the genome browser, facilitating gene re-annotation by individual users.
  
  
  CONCLUSIONS
  The SGR database was developed to facilitate dissemination and data mining of extensive floral and fruit transcriptome data in the woodland strawberry. It enables users to mine the data in different ways to study different pathways or biological processes during reproductive development.
authors.forename: Omar
authors.initials: O
authors.lastname: Darwish
authors.forename: Janet P
authors.initials: JP
authors.lastname: Slovin
authors.forename: Chunying
authors.initials: C
authors.lastname: Kang
authors.forename: Courtney A
authors.initials: CA
authors.lastname: Hollender
authors.forename: Aviva
authors.initials: A
authors.lastname: Geretz
authors.forename: Sam
authors.initials: S
authors.lastname: Houston
authors.affiliation: Department of Computer and Information Sciences, Towson University, 7800 York Road, Towson, MD 21252, USA. ZLIU@UMD.EDU.
authors.forename: Zhongchi
authors.initials: Z
authors.lastname: Liu
authors.forename: Nadim W
authors.initials: NW
authors.lastname: Alkharouf
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D031985:Fragaria / Q000235:genetics*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D023281:Genomics; D020407:Internet