Sequencing information has produced important data that is being used to investigate both basic and applied aspects of plant growth and development. It is the first step towards a functional genomics, and a basic tool for molecular breeding. However, this information has been mainly generated either in model species or species with great impact in global food supply. Fruits of cultivated strawberry (F. xananassa) are appreciated both as fresh and as processed foods. However, there have been only limited genetic and genomic resources developed in this species due to its growing characteristics and the inherent difficulty of working with an octoploid. Despite this, genetic and genomic information is slowly appearing and recently the first genetic map has been reported . In this work we analyzed more than 10,000 ESTs from F. xananassa, assembled in more than 7,000 unigenes. Half of these sequences proceeded from our own sequencing project; a second set of sequences was obtained from the GenBank dbEST Database.
Regarding the new sequences reported here it is worth emphasizing that they proceed from different fruit parts (achenes and receptacle), at different developmental stages (green and red fruit), and after hormone treatment (ethylene). In addition to the genetic characteristics, difficulties analyzing strawberry fruit growth and ripening arise from the fact that the commercial fruit is not a true fruit but includes an engrossed flower receptacle with the true fruits, the achenes, attached on its surface. Moreover, the development pattern of these two parts of the commercial fruit is not synchronous in that the achenes reach their mature stage much earlier than receptacle  Thus, the sequence information provided in this report specific for achenes and receptacle libraries is highly valuable. This is highlighted by the high number of ESTs encoding prunins in the achene library that is absent in the receptacle library. Similarly a large number of ESTs encoding metallothioneins were identified in the receptacle library with a low number of ESTs in the achene library. Prunins are known as the globulins of the genus Prunus, which comprise the main family of storage proteins synthesized in seeds during embryogenesis . Metallothioneins belong to a family of cysteine-rich, low molecular weight proteins that have the capacity to bind metals through the thiol group of the cysteine residues, which represent nearly 30% of their amino acidic residues. These proteins have been shown to be involved in metal scavenging and detoxification , as well as in biotic and abiotic plant responses , . Their high abundance in green receptacle suggests their important role in this organ.
The gene index analysis of the sequences reflected the genetic proximity of strawberry with other species of Rosaceae. Effectively, Fragaria sp. belongs to the Rosaceae family that includes apple, peach and apricot, and to the Rosaceae supertribe  that includes rose. The highest identity in the alignment was with F. vesca, from the same genus, followed by Rosa hybrida from the same supertribe, and Prunus and Malus from the same family. Previous studies on genomic resources of Fragaria and Rosa have also shown a high level of genetic proximity , . There are more than 50.000 ESTs available from the diploid F. vesca  that has been proposed as a model plant for genomic studies. Recent studies have predicted approximately 200 Mb for its genome size  which might facilitate its complete sequencing. However, cultivated strawberry is an octoploid species with at least two genomes involved in its origin; one is thought to be an ancestor of F. vesca or F. manchurica, and the other an ancestor of F. iinumae, or potentially other species .
Overall comparison between the F. vesca and F. xananassa has revealed that only 32.42% of the diploid species had a corresponding putative orthologous gene in the octoploid. A possible explanation for this low value would be that the F. vesca derived subgenome is silenced in F. xananassa, as it has been previously described for specific genes , or even that the donor subgenome could be an ancestor or F. vesca. However, these hypothesis needs further studies since it could also be just a consequence of the different precedence of the EST sequences used in this comparison, mostly from plantlets in F. vesca and from fruits in F. xananassa. In any case, cultivated strawberry still represents a great potential source of alleles that might be important for selected traits, since in other species it has been shown that polyploidization is accompanied by changes in the gene expression, and accordingly in phenotypic variation .
In addition, the strawberry fruit produces some metabolites that are not found in other fruit models, such as tomato. These aspects make the ESTs information provided here valuable since it might eventually be used to probe for specific genes in other species, some of them closely related as some berries of the Rubus genus, like raspberry and blackberry that are classified in the same supertribe of Rosoideae as Fragaria .
SSRs derived from ESTs have been used as functional markers in the generation of maps and in breeding programs. In strawberry, we have previously used some of these markers to study genetic diversity within the species . Based on the high level of identity found with corresponding genes of genetically close species, like those of the Rosaceae family, we foresee their transferability to these species, as other authors have shown , . For this purpose, it is important to indicate that strawberry comparative map reveals a high level of co-linearity between diploid and octoploid Fragaria species . For other species of the Rosaceae family this transferability deserves to be evaluated.
The function played by hormones in the development of strawberry fruits is still an unresolved question. Considered as a non-climacteric fruit, the main role has been attributed to the auxin synthesized in the achenes . A search for genes involved in hormones response was performed. Auxin response factors (ARF) are transcription factors acting on the signalling pathway of this hormone . We have unequivocally identified two of them in the strawberry ESTs Database, FaARF1 and FaARF3. For the FaARF1, the highest homology corresponds to a gene expressed in tomato , and to the Arabidopsis ARF1 gene . FaARF3 has high homology to both ARF3 genes from tomato and Arabidopsis. The strawberry gene FaARF3 is mostly expressed in the receptacle at the white stage. At this stage the content of auxin is decreasing but still high in comparison to red fruits , , and cell expansion determines the final size of the receptacle.
The ethylene binding factors (ERF) constitute a family of transcription factors that were identified by their capacity to bind ethylene-responsive elements (ERE) present as cis -sequences in the ethylene-inducible genes. Further studies revealed that they act as transcriptional activators or repressors of GCC Box-mediated gene expression . In tomato fruits it has been reported that some of them participate in the signalling pathway initiated by ethylene during the ripening of the fruits . In the ESTs collection we have identified three putative ERFs (FaERF1, FaERF2, FaERF3) proceeding from the library prepared from the achenes, and this is consistent with the finding that achenes produced four to ten-fold more ethylene than fruit epidermal peels . Both FaERF1 and FaERF3 have highest expression at the green stage and show high homology with SlERF2  and MdERF1 , respectively, involved in tomato and apple fruit ripening. The corresponding Arabidopsis genes for FaEFR1 and FaERF3 belong to the subfamily B-2 (Group VII) . In contrast, the Arabidopsis gene homologous to FaERF2, which shows minor variation, is classified in the subfamily B-3 (Group IX) . The genes in group IX have often been linked in defensive gene expression in response to pathogen infection.
In strawberry there is no information on the content of active brassinosteroid in the ripening fruit. The preferential expression of FaBRI1 in red receptacle suggests an increased concentration of this hormone in this tissue at later stages of ripening. However, a relationship between FaBRI1 expression and an increased concentration is not direct since it is needed to know the expression of other important elements in the brassinosteroid signalling pathway such as BAK1 (BRI1 associated receptor kinase) and BKI1 (inhibitor of the association of BRI1 and BAK1) . BZR1 is a transcription factor  whose cell location depends on its phosphorylation status, mainly controlled by BIN2 . When BZR1 is phosphorylated goes to the nucleus where induces the expression of brassinosteroid dependent genes. Expression of genes FaBZR and FaBIN2 occurs in achenes and receptacle at all stages, but the expression ratio FaBZR/FaBIN2 is higher in the white achene and lower in white receptacle. These expression patterns must be interpreted under the light of the interaction of the encoded proteins as above indicated. In summary, the functional relevance of all these expression studies in terms of the role of hormones in fruit ripening is limited. However, they illustrate the possibility of using the sequence information here reported to initiate the molecular dissection the problem with gene-specific tools.
The database here reported allowed the comparison of the transcriptome in the ripe receptacle of F. xananassa (cv. Camarosa) and the diploid F. vesca. As expected, there are very specific changes in genes related to secondary metabolism (see Additional file 6). However, global analysis revealed that differences in the transcriptomes being more quantitative than qualitative i.e. supported by activation/depletion rather than by gain/loss of biological processes. The two minor differences found in "response to stress", up-regulated in F. vesca, and "regulation of cellular processes", up-regulated in F. xananassa, are probably related to the domestication of the species. Natural environment of the wild F. vesca is more cold climate and high altitude than F. xananassa , and it is probable that its cultivation under temperate conditions triggers the heat stress response. On the other hand, is not surprising that hormone signalling pathways are more efficient in F. xananassa especially those related to auxin action since it has been reported that increasing auxin content in both F. xananassa and F. vesca has the effect of increasing weight and size of fruits . The relevance of these changes here reported deserves further investigation by a deep study of specific genes. This is currently under progress.