ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species


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.


DOI: 10.3389/fmolb.2020.591406

Projects: Systems toxicology of Atlantic cod

Publication type: Journal

Journal: Frontiers in Molecular Biosciences

Citation: Front. Mol. Biosci. 7,591406

Date Published: 26th Nov 2020

Registered Mode: by DOI

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Hanna, E. M., Zhang, X., Eide, M., Fallahi, S., Furmanek, T., Yadetie, F., Zielinski, D. C., Goksøyr, A., & Jonassen, I. (2020). ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species. In Frontiers in Molecular Biosciences (Vol. 7). Frontiers Media SA.

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Created: 19th May 2021 at 09:19

Last updated: 19th May 2021 at 09:21

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