SGR: an online genomic resource for the woodland strawberry

BMC Plant Biology

Database

Courtney A Hollender¹  Zhongchi Liu¹  Aviva Geretz¹  Chunying Kang¹  Sam Houston²  Nadim W Alkharouf²  Omar Darwish²  Janet P Slovin³ 

[1]Department of Cell Biology and Molecular Genetics, University of Maryland, 0229 Biological Science Research Building, 20742, College Park, MD, USA

[2]Department of Computer and Information Sciences, Towson University, 7800 York Road, 21252, Towson, MD, USA

[3]USDA/ARS Genetic Improvement of Fruits and Vegetables Laboratory, BARC-W 10300 Baltimore Ave, 20705, Beltsville, MD, USA

关键词: Strawberry;    Transcriptome;    RNA-seq;    Database;    gBrowse;    Fruit;    Flowers;    Rosaceae;   

DOI  :  10.1186/1471-2229-13-223

 received in 2013-10-28, accepted in 2013-12-18,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundFragaria 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.DescriptionSGR 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Darwish et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.