Figshare+
Browse
1/1
6 files

Genomes and Annotations of 1,154 budding yeasts

Version 2 2024-04-04, 20:27
Version 1 2024-03-12, 21:57
dataset
posted on 2024-04-04, 20:27 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 contains the genomes and annotations for the 1,154 budding yeasts that were sequenced or re-annotated in this project. 


  • y1000p_cds_files.tar.gz - Fasta files of the nucleotide sequences for the gene annotations in the format assembly_fullID.final.cds
  • y1000p_gff3_files.tar.gz - GFF3 files of the gene annotations in the format assembly_fullID.final.gff3
  • y1000p_gtf_files.tar.gz - GTF files of the gene annotations in the format assembly_fullID.final.gtf
  • y1000p_pep_files.tar.gz - Fasta files of the amino acid sequences for the gene annotations in the format assembly_fullID.final.pep
  • y1000p_genome_files.zip - Fasta files of the assembled genome sequences in the format assembly_fullID.fas.gz

Funding

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

Find out more...

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

Find out more...

Great Lakes Bioenergy Research Center

Office of Biological and Environmental Research

Find out more...

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

I confirm the files and description shared may be publicly distributed under the license selected

  • 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.