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Database (2009) Vol. 2009:bap009; doi:10.1093/database/bap009 published on August 4, 2009
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© 2009 The Author(s).
This is Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs

L. Wissler1, E. Dattolo2,3, A. D. Moore1, T. B. H. Reusch4, J. L. Olsen5, M. Migliaccio2, E. Bornberg-Bauer1 and G. Procaccini2,*

1Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, D48149 Münster, Germany, 2Stazione Zoologica A Dohrn, Villa Comunale, 80121 Naples, 3Dipartimento di Ecologia, Universita della Calabria, Rende (CS), Italy, 4Leibniz-Institut für Meereswissenschaften IFM-Geomar, Düsternbrooker Weg 20, D24105 Kiel, Germany and 5Department of Marine Benthic Ecology and Evolution, Centre for Ecological and Evolutionary Studies, University of Groningen, Biological Centre, 9750 AA Haren, The Netherlands

*Corresponding author: Email: gpro{at}szn.it


  Abstract

As ecosystem engineers, seagrasses are angiosperms of paramount ecological importance in shallow shoreline habitats around the globe. Furthermore, the ancestors of independent seagrass lineages have secondarily returned into the sea in separate, independent evolutionary events. Thus, understanding the molecular adaptation of this clade not only makes significant contributions to the field of ecology, but also to principles of parallel evolution as well. With the use of Dr. Zompo, the first interactive seagrass sequence database presented here, new insights into the molecular adaptation of marine environments can be inferred. The database is based on a total of 14 597 ESTs obtained from two seagrass species, Zostera marina and Posidonia oceanica, which have been processed, assembled and comprehensively annotated. Dr. Zompo provides experimentalists with a broad foundation to build experiments and consider challenges associated with the investigation of this class of non-domesticated monocotyledon systems. Our database, based on the Ruby on Rails framework, is rich in features including the retrieval of experimentally determined heat-responsive transcripts, mining for molecular markers (SSRs and SNPs), and weighted key word searches that allow access to annotation gathered on several levels including Pfam domains, GeneOntology and KEGG pathways. Well established plant genome sites such as The Arabidopsis Information Resource (TAIR) and the Rice Genome Annotation Project are interfaced by Dr. Zompo. With this project, we have initialized a valuable resource for plant biologists in general and the seagrass community in particular. The database is expected to grow together with more data to come in the near future, particularly with the recent initiation of the Zostera genome sequencing project.

The Dr. Zompo database is available at http://drzompo.uni-muenster.de/

Received February 10, 2009; Revised June 23, 2009; Accepted June 29, 2009


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