Strawberry Genome/Transcriptome
The genome of woodland strawberry (Fragaria vesca)
This study is both whole genome and transcriptome analysis of Strawberry (Fragaria vesca).  The F. vesca diploid genome has been sequenced to 39* coverage using NextGen technology and de novo assembly. Transcriptome has been mapped at single base resolution. This data represents Illumina short read data subset of the F. vesca genomic DNA and transcriptome.    "The RNA was isolated from different tissues of diploid woodland strawberry F. vesca  using “RNAeasy Mini Plant RNA kit” (Qiagen) according to the manufacturer’s protocol. The RNA was isolated from young leaves, mature leaves, petioles, crowns, flowers, stolons, runner tips, maturing fruits, and roots. To increase representation of tissue-specific transcripts, approximately equal amounts of total RNA from these tissues were pooled together.
The woodland strawberry, Fragaria vesca (2n=2x=14), represents a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (206Mb), is amenable to genetic transformation, and shares substantial sequence identity with cultivated strawberry (F. × ananassa) and other economic rosaceous plants.  Here we report the draft F. vesca genome, sequenced to 39x coverage using second-generation technology and de novo assembly. Anchorage to the genetic linkage map assembles the genome into seven pseudochromosomes. This diploid strawberry lacks large genome duplications shared among other rosids. Gene prediction modeling identified 34,809 genes, with most supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time are identified. Macro-syntenic relationships between Fragaria and Prunus permit reconstruction of a hypothetical ancestral Rosaceae genome having nine chromosomes.  Inclusion of Fragaria sequence in a phylogenetic analysis of 154 protein-coding genes suggests that Populus should be reassigned from Fabidae to Malvidae.