ArticleBiomolecules2022
A Pan-Draft Metabolic Model Reflects Evolutionary Diversity across 332 Yeast Species.
Article in Biomolecules, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Gempipe: a tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models.mSystems · 2026Article
- Evolution and applications of genome-scale metabolic models in yeast systems biology studies.FEMS yeast research · 2025Review
- pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes.Genome biology · 2024Article
- Panera: An innovative framework for surmounting uncertainty in microbial community modeling using pan-genera metabolic models.iScience · 2024Article
- A genome-informed higher rank classification of the biotechnologically important fungal subphylumStudies in mycology · 2023Article
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Authors and funding
3 authors.
Funding
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Abstract
Yeasts are increasingly employed in synthetic biology as chassis strains, including conventional and non-conventional species. It is still unclear how genomic evolution determines metabolic diversity among various yeast species and strains. In this study, we constructed draft GEMs for 332 yeast species using two alternative procedures from the toolbox RAVEN v 2.0. We found that draft GEMs could reflect the difference in yeast metabolic potentials, and therefore, could be utilized to probe the evolutionary trend of metabolism among 332 yeast species. We created a pan-draft metabolic model to account for the metabolic capacity of every sequenced yeast species by merging all draft GEMs. Further analysis showed that the pan-reactome of yeast has a "closed" property, which confirmed the great conservatism that exists in yeast metabolic evolution. Lastly, the quantitative correlations among trait similarity, evolutionary distances, genotype, and model similarity were thoroughly investigated. The results suggest that the evolutionary distance and genotype, to some extent, determine model similarity, but not trait similarity, indicating that multiple mechanisms shape yeast trait evolution. A large-scale reconstruction and integrative analysis of yeast draft GEMs would be a valuable resource to probe the evolutionary mechanism behind yeast trait variety and to further refine the existing yeast species-specific GEMs for the community.
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