Genomes and Annotations of 1,154 budding yeasts

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

生物体在生态位广度方面表现出广泛的变异，从极为狭窄（专性生物）到极为广泛（广温性生物）不等。用以解释这种变异的范式，要么涉及性能效率与广度之间的权衡，要么涉及潜在的内禀或外在因素。我们收集了来自古真菌亚门Saccharomycotina几乎所有已知物种的基因组（1,090种物种的1,154个酵母菌株）、代谢组（在24种条件下843种物种的生长量的定量测量）和生态组（1,088种物种的环境本体）数据，以考察生态位广度的进化。我们发现，碳广度在种间存在显著差异，这源于编码特定代谢途径的基因的内禀差异，但未发现权衡的证据以及外在生态因素的作用有限。这些全面的数据表明，驱动微生物生态位广度变异的内禀因素起着决定性作用。该数据项包含该项目中测序或重新注释的1,154个酵母菌的基因组及其注释信息。

y1000p_cds_files.tar.gz - 基因注释的核酸序列的Fasta文件，格式为assembly_fullID.final.cds
y1000p_gff3_files.tar.gz - 基因注释的GFF3文件，格式为assembly_fullID.final.gff3
y1000p_gtf_files.tar.gz - 基因注释的GTF文件，格式为assembly_fullID.final.gtf
y1000p_pep_files.tar.gz - 基因注释的氨基酸序列的Fasta文件，格式为assembly_fullID.final.pep
y1000p_genome_files.zip - 组装基因组序列的Fasta文件，格式为assembly_fullID.fas.gz