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: Article in Journal/Newspaper
Language:English
Published: Frontiers 2020
Subjects:
Online Access:https://hdl.handle.net/11250/2730376
https://doi.org/10.3389/fmolb.2020.591406
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spelling ftunivbergen:oai:bora.uib.no:11250/2730376 2023-05-15T15:27:33+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 application/pdf https://hdl.handle.net/11250/2730376 https://doi.org/10.3389/fmolb.2020.591406 eng eng Frontiers Norges forskningsråd: 248840 urn:issn:2296-889X https://hdl.handle.net/11250/2730376 https://doi.org/10.3389/fmolb.2020.591406 cristin:1869909 Navngivelse 4.0 Internasjonal http://creativecommons.org/licenses/by/4.0/deed.no Copyright: Hanna, Zhang, Eide, Fallahi, Furmanek, Yadetie, Zielinski, Goksøyr and Jonassen 591406 Frontiers in Molecular Biosciences 7 345-? Journal article Peer reviewed 2020 ftunivbergen https://doi.org/10.3389/fmolb.2020.591406 2023-03-14T17:41:21Z 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. publishedVersion Article in Journal/Newspaper atlantic cod Gadus morhua University of Bergen: Bergen Open Research Archive (BORA-UiB) Frontiers in Molecular Biosciences 7
institution Open Polar
collection University of Bergen: Bergen Open Research Archive (BORA-UiB)
op_collection_id ftunivbergen
language English
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. publishedVersion
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
publishDate 2020
url https://hdl.handle.net/11250/2730376
https://doi.org/10.3389/fmolb.2020.591406
genre atlantic cod
Gadus morhua
genre_facet atlantic cod
Gadus morhua
op_source 591406
Frontiers in Molecular Biosciences
7
345-?
op_relation Norges forskningsråd: 248840
urn:issn:2296-889X
https://hdl.handle.net/11250/2730376
https://doi.org/10.3389/fmolb.2020.591406
cristin:1869909
op_rights Navngivelse 4.0 Internasjonal
http://creativecommons.org/licenses/by/4.0/deed.no
Copyright: Hanna, Zhang, Eide, Fallahi, Furmanek, Yadetie, Zielinski, Goksøyr and Jonassen
op_doi https://doi.org/10.3389/fmolb.2020.591406
container_title Frontiers in Molecular Biosciences
container_volume 7
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