Additional files Additional file 1: Detailed information about model i CY1106. Additional file 2: Shared reactions between Vongsangnak’s model and i CY1106 (not including transport and exchange reactions, no compartments information). Additional file 3: Result of essential genes identified by FBA using minimum growth medium and yeast extract medium. Additional file 4: Simulation result for the capability of usage different carbon and nitrogen sources for i CY1106. Additional file 5: a Figure for the robustness analysis about oxygen and ARA. b Figure about the acetyl-CoA consumption pathways in iCY1106. c Figure for the robustness analysis about glutamate and ARA. Additional file 6: FBA simulation result for the reactions involving NADPH at different ARA levels. Additional file 7: Biomass composition information for M. alpina. Abbreviations ARA Arachidonic acid PUFAs Polyunsaturated fatty acids ME Malic enzyme GSMM Genome-scale metabolic model MNNG N-methyl-N’-nitro-N-nitrosoguanidine DGLA Dihomo-γ-linolenic acid GLA γ-linolenic acid Cb5R NADH-cytochrome b5 reductase FBA Flux balance analysis EPA Eicosapentaenoic acid FVA Flux variability analysis MOMA Minimization of metabolic adjustment MG Minimal growth YE Yeast extract DO Dissolved oxygen ACC Acetyl-CoA carboxylase GAM Growth associated ATP maintenance NGAM Non-growth associated ATP maintenance Competing interests The authors declare that they have no competing interests. Authors’ contributions CY carried out the construction of iCY1106, performed the statistical analysis, and drafted the manuscript. NX carried out literature mining for M. alpina, provided help for the construct of model. HC, YQC and WC provided the refined genome sequence of M. alpina. LL participated in the design of the study and helped to draft the manuscript. All authors read and approved the final manuscript. Acknowledgements The author would like to thank Dr Jens Nielsen, Professor at Chalmers University of Technology, for technological help on the model reconstruction. This work was supported by the Program for Innovative Research Team in University (IRT1249), the Provincial Outstanding Youth Foundation of Jiangsu Province (BK2012002), the National Natural Science Foundation of China (21422602), the Program for Young Talents in China, the National High-Tech R & D Program of China (No. 2014AA021701). The Program for New Century Excellent Talents (NCET-13-0831), the National Natural Science Foundation of China (No. 31125021, No. 21276108), and the Fundamental Research Funds for the Central Universities (No. JUSRP51320B).