Figure 1.
Figure 1.

Tissues used in the construction of MID-tagged libraries. Eight major tissue types were chosen, including leaves, petioles, crowns, roots, fruits, flowers, stolons, and runner tips. Some individual tissue types were further dissected and pooled to enrich representation of minor tissue types (in parentheses), such as root tips, apical meristems, dormant axial buds, leaf veins, or achenes.

 


Figure 2.
Figure 2.

Tissue distribution of the most abundant reads in strawberry corresponding to nuclear genes. Contigs were assembled from reads compiled from the individual tissue types shown. The relative expression level was calculated from normalized libraries.

 


Figure 3.
Figure 3.

Transcripts enriched in runner tips, stolons, flowers, roots, and crowns. Contigs composed of at least 20 reads where 75% were found in the target tissue were considered. Analysis was performed by means of Blastn and Blastx against the nr database. NSS indicates no significant similarity (>1e−8). Asterisk (*) denotes contigs that do not have sequence matches in the diploid strawberry genome and do not have similarity to GenBank nr.

 


Figure 4.
Figure 4.

Fruit-enriched transcripts. Contigs composed of at least 20 reads that occurred at least 75% of the time in the target tissue were considered. Analysis was performed by means of Blastn against the nr database. VC = virtual contig.

 


Figure 5.
Figure 5.

Contigs composed of an approximately equal number of reads across tissue types. The results represent contigs composed of at least 30 reads. Blastx Best Match is a putative annotation based on description of the best hit in Arabidopsis and/or Ricinus. SD is the standard deviation from a mean of 11.11%, the expected mean if the reads were distributed evenly across all nine tissue pools.

 


Figure 6.
Figure 6.

Species distribution of top BLAST matches for specific contigs. Assembled contigs were compared to the nr database by Blastn and matches better than e−20 were reported. It should be noted that the y-axis list exhibits some redundancy (e.g., Lycopersicon esculentum L. and Solanum lycopersicum L.) under different species names.

 


Figure 7.
Figure 7.

Evidence of nonstrawberry organisms present in starting materials. The figure presents the contig, where it is most expressed and the organism of likely origin. Common pests, symbionts, arthropods, and other organisms are identified. A variety of expected and unexpected relationships are observed.

 


Figure 8.
Figure 8.

Representation of contigs in major GO categories as determined by Blast2GO. A. Biological process, B. Molecular function C. Cellular compartment.