FxaTranscriptome
A Transcript Accounting from Diverse Tissues of a Cultivated Strawberry (Fragaria ×ananassa)
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 the available expressed sequence information in the genus by examining the transcriptome of the cultivated strawberry (Fragaria ×ananassa). To maximize transcript diversity and discovery, plants representing an octoploid strawberry cultivar were subjected to a broad range of environmental stresses, light conditions, hormone treatments, pharmacological challenges, and physical treatments. Plant materials were pooled by tissue type into eight major tissue types, with selected dissections of minor tissues combined into a ninth pool. cDNA pools were sequenced using the Roche-454 GS-FLX system and the resultant sequences were assembled into over thirty-two thousand contigs. Predictions of cellular localization and function were made by associating transcript contigs to annotated homologs, and the tissue pool tags provided a means to estimate gross expression patterns of any given transcript. Contigs comprised of reads originating from only one organ type and those present equally in all plant organs have been identified.  Contaminating bacterial and fungal sequences provide a metagenomic survey of the microbial community of a greenhouse strawberry plant. This study utilizes an innovative assembly strategy on pooled tissues, thus providing a basis for development of tissue-specific tools, a means to identify alleles for marker-assisted selection, a reference of strawberry gene annotations, and a basis for comparative transcriptomics between cultivated strawberry and its diploid ancestors.