title: Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.
abstract: 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/.
authors: Department of Computer Science, University of Helsinki, Helsinki, Finland ; Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland.
authors: Esa
authors: E
authors: Pitkänen
authors: VTT Technical Research Centre of Finland, Espoo, Finland.
authors: Paula
authors: P
authors: Jouhten
authors: Department of Computer Science, University of Helsinki, Helsinki, Finland ; Department of Information and Computer Science, Aalto University, Espoo, Finland.
authors: Jian
authors: J
authors: Hou
authors: VTT Technical Research Centre of Finland, Espoo, Finland.
authors: Muhammad Fahad
authors: MF
authors: Syed
authors: VTT Technical Research Centre of Finland, Espoo, Finland.
authors: Peter
authors: P
authors: Blomberg
authors: Department of Information and Computer Science, Aalto University, Espoo, Finland.
authors: Jana
authors: J
authors: Kludas
authors: VTT Technical Research Centre of Finland, Espoo, Finland.
authors: Merja
authors: M
authors: Oja
authors: Institute of Biotechnology & Department of Biosciences, University of Helsinki, Helsinki, Finland.
authors: Liisa
authors: L
authors: Holm
authors: VTT Technical Research Centre of Finland, Espoo, Finland.
authors: Merja
authors: M
authors: Penttilä
authors: Department of Information and Computer Science, Aalto University, Espoo, Finland.
authors: Juho
authors: J
authors: Rousu
authors: VTT Technical Research Centre of Finland, Espoo, Finland.
authors: Mikko
authors: M
authors: Arvas
mesh_terms: D000465:Algorithms; D018533:Biomass; D001709:Biotechnology; D019295:Computational Biology; D019143:Evolution, Molecular; D005658:Fungi / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D055786:Gene Knockout Techniques; D016681:Genome, Fungal; D007218:Industrial Microbiology; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008954:Models, Biological; D008957:Models, Genetic; D015233:Models, Statistical; D010802:Phylogeny; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D013045:Species Specificity