Open Access Database

AphanoDB: a genomic resource for Aphanomyces pathogens

Mohammed-Amine Madoui1, Elodie Gaulin1, Catherine Mathé1, Hélène San Clemente1, Arnaud Couloux2, Patrick Wincker2 and Bernard Dumas1*

Author Affiliations

1 UMR 5546 CNRS Université Paul Sabatier Toulouse III Pôle de Biotechnologie Végétale 24, Chemin de Borde-Rouge BP 42617, Auzeville 31326 Castanet-Tolosan, France

2 UMR 8030 Génoscope – CNRS, 2 rue Gaston Crémieux, 91000 Evry, France

For all author emails, please log on.

BMC Genomics 2007, 8:471  doi:10.1186/1471-2164-8-471

Published: 20 December 2007

Abstract

Background

The Oomycete genus Aphanomyces comprises devastating plant and animal pathogens. However, little is known about the molecular mechanisms underlying pathogenicity of Aphanomyces species. In this study, we report on the development of a public database called AphanoDB which is dedicated to Aphanomyces genomic data. As a first step, a large collection of Expressed Sequence Tags was obtained from the legume pathogen A. euteiches, which was then processed and collected into AphanoDB.

Description

Two cDNA libraries of A. euteiches were created: one from mycelium growing on synthetic medium and one from mycelium grown in contact to root tissues of the model legume Medicago truncatula. From these libraries, 18,684 expressed sequence tags were obtained and assembled into 7,977 unigenes which were compared to public databases for annotation. Queries on AphanoDB allow the users to retrieve information for each unigene including similarity to known protein sequences, protein domains and Gene Ontology classification. Statistical analysis of EST frequency from the two different growth conditions was also added to the database.

Conclusion

AphanoDB is a public database with a user-friendly web interface. The sequence report pages are the main web interface which provides all annotation details for each unigene. These interactive sequence report pages are easily available through text, BLAST, Gene Ontology and expression profile search utilities. AphanoDB is available from URL: http://www.polebio.scsv.ups-tlse.fr/aphano/ webcite.