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Dataset supporting Figure 2: Phylogenomics

dataset
posted on 2024-03-12, 21:57 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 # 2 in the manuscript. Input files and results from the construction of the phylogenetic tree of the Saccharomycotina subphylum.


Each item contains a README.txt file that gives specific details on the analysis, file structure, and folder structure.


  • y1000p_1403_OG_files.tar.gz - The 1403 ortho groups used to construct the phylogeny of the subphylum
  • 1154yeasts_1403OGs_ml_timetree.tree - Tree file containing the time tree calibrated phylogeny
  • 1154yeasts_1403OGs_ml_timetree_times.txt - File containing the estimated times associated with the time tree
  • 1175taxa_1403OGs_iqtree_ML_rooted.nex - Nexus tree file containing the rooted tree file used in Figure 2 and the supplemental tree file
  • 1175taxa_1403OGs_astral_length_rooted_lpp_added.tre - Tree file containing the yeast phylogeny estimated using ASTRAL
  • 1000_strip*.txt - iTOL (itol.com) files to identify the isolation environment of the strains.
  • itol_color_strip.txt - Add colors to the tree in iTOL
  • ALL_NAMES_FILE.xlsx - The names on the tree have been adjusted to reflect the most recent naming conventions (as of November 2023). This file contains the matching names across the dataset, including earlier versions of the phylogenetic trees which were used for some analyses



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

I confirm there is no human personally identifiable information in the files or description shared

  • Yes

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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.