AUTHOR=Hanna Eileen Marie , Zhang Xiaokang , Eide Marta , Fallahi Shirin , Furmanek Tomasz , Yadetie Fekadu , Zielinski Daniel Craig , Goksøyr Anders , Jonassen Inge TITLE=ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species JOURNAL=Frontiers in Molecular Biosciences VOLUME=7 YEAR=2020 URL=https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2020.591406 DOI=10.3389/fmolb.2020.591406 ISSN=2296-889X ABSTRACT=

The availability of genome sequences, annotations, and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in bacteria, archaea, and eukaryotes. When modeled using mathematical representations, a reconstruction can simulate underlying genotype-phenotype relationships. Accordingly, genome-scale metabolic models (GEMs) can be used to predict the response of organisms to genetic and environmental variations. A bottom-up reconstruction procedure typically starts by generating a draft model from existing annotation data on a target organism. For model species, this part of the process can be straightforward, due to the abundant organism-specific biochemical data. However, the process becomes complicated for non-model less-annotated species. In this paper, we present a draft liver reconstruction, ReCodLiver0.9, of Atlantic cod (Gadus morhua), a non-model teleost fish, as a practicable guide for cases with comparably few resources. Although the reconstruction is considered a draft version, we show that it already has utility in elucidating metabolic response mechanisms to environmental toxicants by mapping gene expression data of exposure experiments to the resulting model.