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Open Access Highly Accessed Research article

A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica

Nicolas Loira14, Thierry Dulermo23, Jean-Marc Nicaud23 and David James Sherman1*

Author Affiliations

1 Inria / Université Bordeaux / CNRS joint project-team MAGNOME, Talence, F-33405, France

2 INRA, UMR1319 Micalis, Jouy-en-Josas, F-78352, France

3 CNRS, Micalis, Jouy-en-Josas, F-78352, France

4 Center for Genome Regulation, Universidad de Chile, Av. Blanco Encalada 2085, 3er piso, Santiago, Chile

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BMC Systems Biology 2012, 6:35  doi:10.1186/1752-0509-6-35

Published: 4 May 2012

Additional files

Additional file 1:

Table S1 Manual curation of lost reactions. In many cases, orthology results fail to associate a target gene to an enzyme-coding gene in the scaffold model, suggesting that the reaction is absent. Each of these predictions were manually reviewed, where a reaction was confirmed as being absent (‘Lost’), or was upheld (‘Retained’) when empirical evidence was available. Genes for which no ortholog could be found are

    underlined
in the gene association column.

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Additional file 2 :

Table S2 Validation of the iNL895 model. This table lists 152 experiments extracted from the literature, detailing media conditions, gene KOs, and observed growth (as yes/no). It also includes our simulations of the same experiments, obtained using FBA/COBRA Tools, and the comparison between observed and the simulated growth.

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Additional file 3:

Figure S1Projection pipeline from S. cerevisiae scaffold model to Y. lipolytica iNL895. The three main parts of our pipeline for the reconstruction of the Y. lipolytica model are: Projection, where the S. cerevisiae scaffold model and the information from different sources of orthology between S. cerevisiae and Y. lipolytica are used to produce a draft model, Curation, where the expert curators revised the candidates for gap-filling and added species-specific reactions and Validation, where experiments obtained from the literature were compared with our simulations, producing a detailed accuracy report.

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Additional file 4:

Figure S2 Gene Association rewrite from S. cerevisiae reactions to Y. lipolytica. Pipeline for gene-association rewriting, as part of the projection of Y. lipolytica iNL895 model. From the 4 ortholog maps provided by different methods, a map of votes of possible ortholog mappings is created. Then, from the scaffold model, we extracted gene associations for each reaction, and re-wrote them based on our map of homologs (e.g.: Reaction1: (SourceGene1 or SourceGene2) ↔ (TargetGene1)). The new reactions, this time associated with Y. lipolytica genes, constituted the base of the reconstructed model.

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Additional file 5 :

Selected gene annotations inY. lipolytica. This table lists Y. lipolytica genes used in the manual curation of the metabolic model.

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Additional file 6 :

Complete validation tests forY. lipolytica. This MATLAB file runs the validation tests of the Y. lipolytica metabolic model. It requires the COBRA Toolbox (2.0+). Each of the 152 tests is declared as a MATLAB function, in order to help the curation process. All tests can be ran in batch mode using: matlab -nodisplay -nosplash -nojvm -r “model0=runTests(‘supp_2.xml’, ‘test.results’); exit;”

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Additional file 7 :

Y. lipolyticaiNL895 SBML model. SBML representation of the reconstructed model of Y. lipolytica. This XML file is compatible with SBML Level 2, Version 4, and has been tested with COBRA Toolbox (2.0) and CellDesigner (4.1). This model can also be retrieved from the BioModels database (http://biomodels.org), under model id MODEL1111190000.

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