Abstract
BackgroundSince no genome sequences of solanaceous plants have yet been completed, expressed sequence tag (EST) collections represent a reliable tool for broad sampling of Solanaceae transcriptomes, an attractive route for understanding Solanaceae genome functionality and a powerful reference for the structural annotation of emerging Solanaceae genome sequences.DescriptionWe describe the SolEST database http://biosrv.cab.unina.it/solestdb which integrates different EST datasets from both cultivated and wild Solanaceae species and from two species of the genus Coffea. Background as well as processed data contained in the database, extensively linked to external related resources, represent an invaluable source of information for these plant families. Two novel features differentiate SolEST from other resources: i) the option of accessing and then visualizing Solanaceae EST/TC alignments along the emerging tomato and potato genome sequences; ii) the opportunity to compare different Solanaceae assemblies generated by diverse research groups in the attempt to address a common complaint in the SOL community.ConclusionDifferent databases have been established worldwide for collecting Solanaceae ESTs and are related in concept, content and utility to the one presented herein. However, the SolEST database has several distinguishing features that make it appealing for the research community and facilitates a "one-stop shop" for the study of Solanaceae transcriptomes.
Highlights
Since no genome sequences of solanaceous plants have yet been completed, expressed sequence tag (EST) collections represent a reliable tool for broad sampling of Solanaceae transcriptomes, an attractive route for understanding Solanaceae genome functionality and a powerful reference for the structural annotation of emerging Solanaceae genome sequences.Description: We describe the SolEST database http://biosrv.cab.unina.it/solestdb which integrates different Expressed Sequence Tags (ESTs) datasets from both cultivated and wild Solanaceae species and from two species of the genus Coffea
The SolEST database has several distinguishing features that make it appealing for the research community and facilitates a "one-stop shop" for the study of Solanaceae transcriptomes
We think the SolEST database will represent an invaluable resource for supporting the structural annotation of the emerging Solanaceae genome sequences and addressing technical issues arising while sequencing efforts are being made
Summary
No similar work has yet been carried out on the construction of an EST database offering a broad overview of Solanaceae as well as Coffea transcriptomes. We think the SolEST database will represent an invaluable resource for supporting the structural annotation of the emerging Solanaceae genome sequences and addressing technical issues arising while sequencing efforts are being made. The mapping of Solanaceae ESTs certainly provides insights into the location of potential candidate genes and facilitates EST-driven gene annotation This represents the first attempt to provide a unique view of the data from both the sequencing efforts, which we believe will be appreciated by the SOL community. NDA was mainly involved in the development, organization and maintenance of the SolEST database and wrote the manuscript; AT was involved in setting up the comparative analysis of the genome sequences from tomato and potato; LF contributed to carrying out the project; MLC conceived the project, directed its design and implementation, coordinated the different efforts and wrote the manuscript.
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