Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.

We introduce a novel computational approach, CoReCo, for comparative metabolic reconstruction and provide genome-scale metabolic network models for 49 important fungal species. Leveraging on the exponential growth in sequenced genome availability, our method reconstructs genome-scale gapless metabol...

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Autores principales:	Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko Arvas
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/86ec0bb03c1741418f5839c443b1157e
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spelling	oai:doaj.org-article:86ec0bb03c1741418f5839c443b1157e2021-11-18T05:53:09ZComparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.1553-734X1553-735810.1371/journal.pcbi.1003465https://doaj.org/article/86ec0bb03c1741418f5839c443b1157e2014-02-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24516375/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358We introduce a novel computational approach, CoReCo, for comparative metabolic reconstruction and provide genome-scale metabolic network models for 49 important fungal species. Leveraging on the exponential growth in sequenced genome availability, our method reconstructs genome-scale gapless metabolic networks simultaneously for a large number of species by integrating sequence data in a probabilistic framework. High reconstruction accuracy is demonstrated by comparisons to the well-curated Saccharomyces cerevisiae consensus model and large-scale knock-out experiments. Our comparative approach is particularly useful in scenarios where the quality of available sequence data is lacking, and when reconstructing evolutionary distant species. Moreover, the reconstructed networks are fully carbon mapped, allowing their use in 13C flux analysis. We demonstrate the functionality and usability of the reconstructed fungal models with computational steady-state biomass production experiment, as these fungi include some of the most important production organisms in industrial biotechnology. In contrast to many existing reconstruction techniques, only minimal manual effort is required before the reconstructed models are usable in flux balance experiments. CoReCo is available at http://esaskar.github.io/CoReCo/.Esa PitkänenPaula JouhtenJian HouMuhammad Fahad SyedPeter BlombergJana KludasMerja OjaLiisa HolmMerja PenttiläJuho RousuMikko ArvasPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 10, Iss 2, p e1003465 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Esa Pitkänen Paula Jouhten Jian Hou Muhammad Fahad Syed Peter Blomberg Jana Kludas Merja Oja Liisa Holm Merja Penttilä Juho Rousu Mikko Arvas Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.
description	We introduce a novel computational approach, CoReCo, for comparative metabolic reconstruction and provide genome-scale metabolic network models for 49 important fungal species. Leveraging on the exponential growth in sequenced genome availability, our method reconstructs genome-scale gapless metabolic networks simultaneously for a large number of species by integrating sequence data in a probabilistic framework. High reconstruction accuracy is demonstrated by comparisons to the well-curated Saccharomyces cerevisiae consensus model and large-scale knock-out experiments. Our comparative approach is particularly useful in scenarios where the quality of available sequence data is lacking, and when reconstructing evolutionary distant species. Moreover, the reconstructed networks are fully carbon mapped, allowing their use in 13C flux analysis. We demonstrate the functionality and usability of the reconstructed fungal models with computational steady-state biomass production experiment, as these fungi include some of the most important production organisms in industrial biotechnology. In contrast to many existing reconstruction techniques, only minimal manual effort is required before the reconstructed models are usable in flux balance experiments. CoReCo is available at http://esaskar.github.io/CoReCo/.
format	article
author	Esa Pitkänen Paula Jouhten Jian Hou Muhammad Fahad Syed Peter Blomberg Jana Kludas Merja Oja Liisa Holm Merja Penttilä Juho Rousu Mikko Arvas
author_facet	Esa Pitkänen Paula Jouhten Jian Hou Muhammad Fahad Syed Peter Blomberg Jana Kludas Merja Oja Liisa Holm Merja Penttilä Juho Rousu Mikko Arvas
author_sort	Esa Pitkänen
title	Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.
title_short	Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.
title_full	Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.
title_fullStr	Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.
title_full_unstemmed	Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.
title_sort	comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/86ec0bb03c1741418f5839c443b1157e
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Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.

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