A Transcript Accounting from Diverse Tissues of a Cultivated Strawberry

Strawberry (Fragaria spp.) is a valuable fruit crop as well as an outstanding system for studying functional genomics in plants. The goal of this study was to substantially increase and analyze the available expressed sequence information in the genus by examining the transcriptome of the cultivated strawberry (Fragaria × ananassa Duchesne). To maximize transcript diversity and discovery, plants representing an octoploid strawberry cultivar were subjected to a broad range of treatments. Plant materials were pooled by tissue type. cDNA pools were sequenced by the Roche-454 GS-FLX system and assembled into over 32,000 contigs. Predictions of cellular localization and function were made by associating assembled contigs to annotated homologs, and the tissue pool tags provided a means to assess the overall expression pattern for any given transcript. Contigs comprised of reads originating from only one organ type and those present equally in all plant organs were both identifi ed. Bacterial and fungal sequences found in the strawberry samples provide a metagenomic survey of the microbial community of a greenhouse strawberry plant. This study utilized an innovative assembly strategy on pooled tissues, thus providing a foundation for developing tissue-specifi c tools, an opportunity to identify alleles for marker-assisted selection, a reference of strawberry gene annotations, and a basis for comparative transcriptomics between cultivated strawberry, its diploid ancestors, and the wider Rosaceae family. C ULTIVATED STRAWBERRY is a valuable crop, prized for its fl avorful and nutritious fruits. Strawberry is an important crop for many regional economies worldwide and off ers high levels of healthful compounds. Species within the genus Fragaria occur naturally throughout the northern hemisphere and represent many levels of ploidy, including wild diploids and the wild and cultivated octoploids (reviewed in Folta and Davis, 2006; Hummer and Hancock, 2009). Recent attention has been brought to the diploid strawberry species Fragaria vesca Coville because of its utility as a highly tractable experimental system within the economically important Rosaceae family (Folta and Davis, 2006). Strawberry is emerging as a powerful functional genomics system. Fragaria vesca’s haploid genome size of ~200 Mb is among the smallest of the rosaceous crop plants (Shulaev et al., 2008), and its complete genome sequence will be available in 2010, providing an invaluable resource with reference to its octoploid, cultivated relatives. Most importantly, several genotypes of both diploid and octoploid strawberry are readily transformable, making it an outstanding system for functional studies. Protocols exist for diploid and octoploid lines that allow effi cient regeneration of transgenic materials in a period of weeks to months (Folta and Dhingra, 2006; Mezzetti and