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Genome Analyses of 1,154 budding yeasts

dataset
posted on 2024-03-12, 21:56 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 the raw data for multiple analyses conducted on the genomic data. Each folder contains a readme.txt file that details the analysis and file formats. The analyses included in this folder are


  • annotations_pep_interproscan.zip: InterPro - InterProScan was run on every genome annotation. The raw results are reported for all 1,154 yeasts. 
  • y1000p_codetta_output.tar.gz: Codetta analysis - Codetta was run on every genome to determine the likely genetic code. 
  • y1000p_orthofinder.tar.gz: Orthfinder Results - Orthofinder was run on all genome annotations to create orthogroups 
  •  y1000p_tRNA_scan.tar.gz: tRNAscan Results - tRNAscan was run on each genome assembly to determine the copy number, location and state of tRNAs within the genomes
  • y1000plus_annotations_pep_kegg.tar.gz: KEGG Annotations - KEGG orthology was assigned to each genome annotation. 
  • y1000p_repeatmsker_analysis.tar.gz: Repeatmasker analysis - Repeatmasker was run on all genome assemblies. A masked version of each genome is included in this folder
  • Y1000p_BUCO_fulltable.tar.gz: BUSCO analysis - BUSCO was run on all genome assemblies. The "full table" results are reported for each genome

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

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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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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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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.