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
Other Authors: Norges Forskningsråd
Format: Article in Journal/Newspaper
Language:unknown
Published: Frontiers Media SA 2020
Subjects:
Online Access:http://dx.doi.org/10.3389/fmolb.2020.591406
https://www.frontiersin.org/articles/10.3389/fmolb.2020.591406/full
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spelling crfrontiers:10.3389/fmolb.2020.591406 2024-09-15T17:55:30+00:00 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 Norges ForskningsrÃ¥d 2020 http://dx.doi.org/10.3389/fmolb.2020.591406 https://www.frontiersin.org/articles/10.3389/fmolb.2020.591406/full unknown Frontiers Media SA https://creativecommons.org/licenses/by/4.0/ Frontiers in Molecular Biosciences volume 7 ISSN 2296-889X journal-article 2020 crfrontiers https://doi.org/10.3389/fmolb.2020.591406 2024-07-30T04:01:56Z 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. Article in Journal/Newspaper atlantic cod Gadus morhua Frontiers (Publisher) Frontiers in Molecular Biosciences 7
institution Open Polar
collection Frontiers (Publisher)
op_collection_id crfrontiers
language unknown
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.
author2 Norges Forskningsråd
format Article in Journal/Newspaper
author Hanna, Eileen Marie
Zhang, Xiaokang
Eide, Marta
Fallahi, Shirin
Furmanek, Tomasz
Yadetie, Fekadu
Zielinski, Daniel Craig
Goksøyr, Anders
Jonassen, Inge
spellingShingle 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
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 SA
publishDate 2020
url http://dx.doi.org/10.3389/fmolb.2020.591406
https://www.frontiersin.org/articles/10.3389/fmolb.2020.591406/full
genre atlantic cod
Gadus morhua
genre_facet atlantic cod
Gadus morhua
op_source Frontiers in Molecular Biosciences
volume 7
ISSN 2296-889X
op_rights https://creativecommons.org/licenses/by/4.0/
op_doi https://doi.org/10.3389/fmolb.2020.591406
container_title Frontiers in Molecular Biosciences
container_volume 7
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