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MolliGen, a database dedicated to the
comparative genomics of Mollicutes
Aurélien Barré, 2Pascal Sirand-Pugnet, 2Xavier Foissac,
3Eduardo P. C. Rocha, 1Antoine de Daruvar and 2Alain Blanchard
1
1Centre
de Bioinformatique Bordeaux (CBiB), Université Victor Segalen Bordeaux 2;
2UMR GDPP, INRA-Université Victor Segalen Bordeaux 2
3CNRS URA 2171, Institut Pasteur, Paris-FRANCE
Bacteria belonging to the class Mollicutes were among the first ones to be selected for complete
genome sequencing because of the minimal size of their genome and of their pathogenicity for
humans and a broad range of animals and plants (1,2,3) (Figure 1). Comparative genomics
analysis is difficult to carry out without a suitable platform gathering not only the original
annotations but also relevant information available in public databases or obtained applying
common bioinformatics methods. With the aim of solving these difficulties, we have developed a
web-accessible database named MolliGen.
Original genome data
(GenBank)
External public resources
(NCBI COG, KEGG, )
HTML report
input / output
files
Figure 1 : Mollicute phylogenic tree. In green genomes integrated
in MolliGen,in red others available complete genomes
1st data level (core)
-mapping genes on
metabolic pathway
Structure
2nd data level
-building orthology
relationship
….
Information, extracted from various databases or computed locally, are stored as structured
data in MolliGen relational database, which consists of two levels :
Export
manager
Query, Browse, Visualise
individual genomes
Browse, Visualise, Align
multiple genomes
(comparative genomics)
1. the first one comprising most basic information and stored as the database core
2. the second containing all other computed information (domains, metabolic pathway,
homology, …)
Such a structure (Figure 2) allows to easily add new organisms (by extending the core)
or new information (by extending the second level).
Figure 2 : MolliGen schema for data integration and accession via the web
Query
MolliGen provides access to integrated data through a web form in which
query is dynamically built by the user (Figure 3A). Results can be obtained
either for only one species or globally, with links to other information and
bioinformatic methods (Figure 3B-D).
Comparison
• A multi-genomes browser developed for MolliGen allows to visualize more
than one genome and to display relationships between them.
(Figure 3D)
• A clickable dot-plot representation allows to visualise relationships between
two genomes over their full length.
• A metabolic pathway viewer, based on KEGG predictions (4) for enzymatic
functions, has been developed to show graphically resemblance between
set of genome(s) for a selected pathway.
• A multi proteome differential queries can be performed to find genes
specific for a genome (or a set of genomes) having homologs in a targeted
group of other genomes. (Figure 1E-F). A third group of genomes can be
selected as an exclusion genome set where no homologs must be found.
Conclusion
MolliGen centralizes and integrates heterogeneous information about
mollicutes in a database. New genomes sequences and information will
Figure 3 : MolliGen interface overview
be added as they will become publicly available. This database will also
be used as an aid for the re-annotation of these genomes, using
1.- Frey, J. (2002) Animal mycoplasmas. In Herrmann, R. (ed.), Molecular biology and pathogenicity of
mycoplasmas. Kluwer Academic/Plenum Publishers, London, pp. 73-90.
2. - Blanchard, A. and Bébéar, C.M. (2002) Human mycoplasmas. In Herrmann, R. (ed.), Molecular biology and
pathogenicity of mycoplasmas. Kluwer Academic/Plenum Publishers, London, pp. 45-71.
3. - Bove, J.M., Renaudin, J., Saillard, C., Foissac, X. and Garnier, M. (2003) SPIROPLASMA CITRI, A PLANT
PATHOGENIC MOLLICUTE: Relationships with Its Two Hosts, the Plant and the Leafhopper Vector. Annu Rev
Phytopathol, 41, 483-500.
4. Kanehisa M, Goto S. (2000 ) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 2730.
homology relationship between them.
MolliGen is publicly available at http://cbi.labri.fr/outils/molligen/.