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...

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Published in:Frontiers in Molecular Biosciences
Main Authors: Hanna, Eileen Marie, Zhang, Xiaokang, Eide, Marta, Fallahi, Shirin, Furmanek, Tomasz, Yadetie, Fekadu, Zielinski, Daniel Craig, Goksøyr, Anders, Jonassen, Inge
Format: Text
Language:English
Published: Frontiers Media S.A. 2020
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Online Access:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7726423/
http://www.ncbi.nlm.nih.gov/pubmed/33324679
https://doi.org/10.3389/fmolb.2020.591406
id ftpubmed:oai:pubmedcentral.nih.gov:7726423
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spelling ftpubmed:oai:pubmedcentral.nih.gov:7726423 2023-05-15T15:27:32+02:00 ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species Hanna, Eileen Marie Zhang, Xiaokang Eide, Marta Fallahi, Shirin Furmanek, Tomasz Yadetie, Fekadu Zielinski, Daniel Craig Goksøyr, Anders Jonassen, Inge 2020-11-26 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7726423/ http://www.ncbi.nlm.nih.gov/pubmed/33324679 https://doi.org/10.3389/fmolb.2020.591406 en eng Frontiers Media S.A. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7726423/ http://www.ncbi.nlm.nih.gov/pubmed/33324679 http://dx.doi.org/10.3389/fmolb.2020.591406 Copyright © 2020 Hanna, Zhang, Eide, Fallahi, Furmanek, Yadetie, Zielinski, Goksøyr and Jonassen. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. CC-BY Front Mol Biosci Molecular Biosciences Text 2020 ftpubmed https://doi.org/10.3389/fmolb.2020.591406 2020-12-20T01:29:47Z 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. Text atlantic cod Gadus morhua PubMed Central (PMC) Frontiers in Molecular Biosciences 7
institution Open Polar
collection PubMed Central (PMC)
op_collection_id ftpubmed
language English
topic Molecular Biosciences
spellingShingle Molecular Biosciences
Hanna, Eileen Marie
Zhang, Xiaokang
Eide, Marta
Fallahi, Shirin
Furmanek, Tomasz
Yadetie, Fekadu
Zielinski, Daniel Craig
Goksøyr, Anders
Jonassen, Inge
ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species
topic_facet Molecular Biosciences
description 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.
format Text
author Hanna, Eileen Marie
Zhang, Xiaokang
Eide, Marta
Fallahi, Shirin
Furmanek, Tomasz
Yadetie, Fekadu
Zielinski, Daniel Craig
Goksøyr, Anders
Jonassen, Inge
author_facet Hanna, Eileen Marie
Zhang, Xiaokang
Eide, Marta
Fallahi, Shirin
Furmanek, Tomasz
Yadetie, Fekadu
Zielinski, Daniel Craig
Goksøyr, Anders
Jonassen, Inge
author_sort Hanna, Eileen Marie
title ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species
title_short ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species
title_full ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species
title_fullStr ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species
title_full_unstemmed ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species
title_sort recodliver0.9: overcoming challenges in genome-scale metabolic reconstruction of a non-model species
publisher Frontiers Media S.A.
publishDate 2020
url http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7726423/
http://www.ncbi.nlm.nih.gov/pubmed/33324679
https://doi.org/10.3389/fmolb.2020.591406
genre atlantic cod
Gadus morhua
genre_facet atlantic cod
Gadus morhua
op_source Front Mol Biosci
op_relation http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7726423/
http://www.ncbi.nlm.nih.gov/pubmed/33324679
http://dx.doi.org/10.3389/fmolb.2020.591406
op_rights Copyright © 2020 Hanna, Zhang, Eide, Fallahi, Furmanek, Yadetie, Zielinski, Goksøyr and Jonassen.
http://creativecommons.org/licenses/by/4.0/
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
op_rightsnorm CC-BY
op_doi https://doi.org/10.3389/fmolb.2020.591406
container_title Frontiers in Molecular Biosciences
container_volume 7
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