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Dataset supporting Figure 4: Metabolism

dataset
posted on 2024-03-12, 21:58 authored by Dana OpulenteDana Opulente, Abigail LaBellaAbigail LaBella, Chris Todd HittingerChris Todd Hittinger, Antonis Rokas, Marie-Claire Harrison, John F. Wolters, Chao Liu, Jacek Kominek, Jacob SteenwykJacob Steenwyk, Margarida Silva, Carla GonçalvesCarla Gonçalves, Yuanning LiYuanning Li, Amanda Beth Hulfachor, Xiaofan ZhouXiaofan Zhou, Xing-Xing ShenXing-Xing Shen, Yonglin Li, Marizeth Groenewald

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,090 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation.


This item includes raw and underlying data associated with Figure 4 in the manuscript.


These items were used to assess differences in metabolic networks between generalist and specialist yeasts.


Each item includes a README.txt file that includes specific information about the analysis, file structure, and folder structure.


  • Y1000_XYL3_DNA.FASTA - This is a FASTA file with the custom XYL3 annotations used to measure presence and absence in the generalists and specialist yeasts. Sequences are labeled with the assembly_ID
  • ALL_BBH1_seq.prot.fasta - This is a FASTA file with the custom BBH1 annotations used to measure presence and absence in the generalist and specialist yeasts. Sequences are labeled with the assembly_ID and gene ID.
  • AllClassification_EdgeList.rda - This is a .RDA file that contains the KEGG annotation edge list for all yeast strains that can be used to build metabolic networks for each yeast strain. When loaded, it will open up a list where is item in the list is the edge list for the strain. Strains are named by their annotation name.
  • GenSpec_KEGG_NetworkStats.xlsx - This is an excel file that contains all of thenetwork statistics calculated for each yeast strain and their carbon classification. We calculated - assortativity, betweenness, density, diameter, edge count, and modularity for each yeast.
  • Y1000_KEGG_Annotations.xlsx - This is an excel file that contains a matrix for KEGG annotation presence (n = 1) and absence (n = 0) for all yeast strains.
  • Specialist Fermentation Carnitine Data.xlsx - This is an excel file that contains the number of specialists which can and cannot grow on a specific carbon source when they have and do not have the full carnitine pathway.
  • Specialist Fermentation Carninitine Results.xlsx - This is an excel file with the results from the proportion test for each carbon source which tests the number of specialists that can and cannot grow on a carbon source with and without full carnitine pathways.
  • RandomForestCode_GenSpec.ipynb - Random forest code for the classification of carbon generalists and specialists based on KEGG features

Funding

DIMENSIONS: Collaborative Research: The Making of Biodiversity Across the Yeast Subphylum

Directorate for Biological Sciences

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Collaborative Research: RoL: The Evolution of the Genotype-Phenotype Map across Budding Yeasts

Directorate for Biological Sciences

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DIMENSIONS: Collaborative Research: The Making of Biodiversity Across the Yeast Subphylum

Directorate for Biological Sciences

Find out more...

Collaborative Research: RoL: The Evolution of the Genotype-Phenotype Map across Budding Yeasts

Directorate for Biological Sciences

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Great Lakes Bioenergy Research Center

Office of Biological and Environmental Research

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Hatch Project 1020204

History

Research Institution(s)

UW-Madison; Villanova; Vanderbilt; UNC Charlotte; Zhejiang U.; South China Agricultural U.; UC Berkeley; U. NOVA de Lisboa; Shandong U.; Zhejiang U.; Westerdijk Fungal Biodiversity Institute

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  • Yes

Competing Interest Statement

J.L.S. is a scientific adviser for WittGen Biotechnologies and an adviser for ForensisGroup Inc. A.R. is a scientific consultant for LifeMine Therapeutics, Inc. J.K. is an employee of LifeMine Therapeutics, Inc. The other authors declare no other competing interests.