biostudies-literatureUnknown9Dinh HVU.S. Department of Energy<i>Rhodosporidium toruloides</i> is a red, basidiomycetes yeast that can accumulate a large amount of lipids and produce carotenoids. To better assess this non-model yeast's metabolic capabilities, we reconstructed a genome-scale model of <i>R. toruloides</i> IFO0880's metabolic network (<i>iRhto</i>1108) accounting for 2204 reactions, 1985 metabolites and 1108 genes. In this work, we integrated and supplemented the current knowledge with in-house generated biomass composition and experimental measurements pertaining to the organism's metabolic capabilities. Predictions of genotype-phenotype relations were improved through manual curation of gene-protein-reaction rules for 543 reactions leading to correct recapitulations of 84.5% of gene essentiality data (sensitivity of 94.3% and specificMetabolic engineering communicationse00101https://www.ebi.ac.uk/biostudies/studies/S-EPMC6838544biostudies-literatureA comprehensive genome-scale model for <i>Rhodosporidium toruloides</i> IFO0880 accounting for functional genomics and phenotypic data.PMC6838544Rabinowitz JDRao CVJagtap SSDeewan AShen YXiao TMaranas CDDinh HVSuthers PFChan SHJZhao HfalseA comprehensive genome-scale model for <i>Rhodosporidium toruloides</i> IFO0880 accounting for functional genomics and phenotypic data.<i>Rhodosporidium toruloides</i> is a red, basidiomycetes yeast that can accumulate a large amount of lipids and produce carotenoids. To better assess this non-model yeast's metabolic capabilities, we reconstructed a genome-scale model of <i>R. toruloides</i> IFO0880's metabolic network (<i>iRhto</i>1108) accounting for 2204 reactions, 1985 metabolites and 1108 genes. In this work, we integrated and supplemented the current knowledge with in-house generated biomass composition and experimental measurements pertaining to the organism's metabolic capabilities. Predictions of genotype-phenotype relations were improved through manual curation of gene-protein-reaction rules for 543 reactions leading to correct recapitulations of 84.5% of gene essentiality data (sensitivity of 94.3% and specific2019-01-01T00:00:00Z2019 Dec2026-07-14T13:38:33.997Z2026-06-19T03:07:42.69ZS-EPMC68385443172021610.1016/j.mec.2019.e00101