AphanoDB: a genomic resource for <it>Aphanomyces </it>pathogens

BMC Genomics. 2007;8(1):471 DOI 10.1186/1471-2164-8-471

 

Journal Homepage

Journal Title: BMC Genomics

ISSN: 1471-2164 (Online)

Publisher: BMC

LCC Subject Category: Technology: Chemical technology: Biotechnology | Science: Biology (General): Genetics

Country of publisher: United Kingdom

Language of fulltext: English

Full-text formats available: PDF, HTML

 

AUTHORS

Wincker Patrick
Couloux Arnaud
San Clemente Hélène
Mathé Catherine
Gaulin Elodie
Madoui Mohammed-Amine
Dumas Bernard

EDITORIAL INFORMATION

Blind peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 17 weeks

 

Abstract | Full Text

<p>Abstract</p> <p>Background</p> <p>The Oomycete genus <it>Aphanomyces </it>comprises devastating plant and animal pathogens. However, little is known about the molecular mechanisms underlying pathogenicity of <it>Aphanomyces </it>species. In this study, we report on the development of a public database called AphanoDB which is dedicated to <it>Aphanomyces </it>genomic data. As a first step, a large collection of Expressed Sequence Tags was obtained from the legume pathogen <it>A. euteiches</it>, which was then processed and collected into AphanoDB.</p> <p>Description</p> <p>Two cDNA libraries of <it>A. euteiches </it>were created: one from mycelium growing on synthetic medium and one from mycelium grown in contact to root tissues of the model legume <it>Medicago truncatula</it>. 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.</p> <p>Conclusion</p> <p>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: <url>http://www.polebio.scsv.ups-tlse.fr/aphano/</url>.</p>