Genomes and Annotations of 1,154 budding yeasts

<strong>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</strong>. 
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This item contains the genomes and annotations for the 1,154 budding yeasts that were sequenced or re-annotated in this project. 
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<strong>y1000p_cds_files.tar.gz</strong> - Fasta files of the nucleotide sequences for the gene annotations in the format assembly_fullID.final.cds
<strong>y1000p_gff3_files.tar.gz</strong> - GFF3 files of the gene annotations in the format assembly_fullID.final.gff3
<strong>y1000p_gtf_files.tar.gz</strong> - GTF files of the gene annotations in the format assembly_fullID.final.gtf
<strong>y1000p_pep_files.tar.gz</strong> - Fasta files of the amino acid sequences for the gene annotations in the format assembly_fullID.final.pep
<strong>y1000p_genome_files.zip</strong> - Fasta files of the assembled genome sequences in the format assembly_fullID.fas.gz

生物体的生态位广度（ecological niche breadth）存在广泛变异，涵盖从极窄的特化种（specialists）到极宽的泛化种（generalists）的连续谱系。学界已提出多种范式阐释这一变异：要么认为其源于性能效率与生态位广度间的进化权衡，要么归因于内在或外在驱动因素。本研究收集了古老真菌亚门——酿酒酵母亚门（Saccharomycotina）几乎所有已知物种的多组学数据：包括1154株酵母菌（隶属于1090个物种）的基因组数据、24种培养条件下843个物种生长量定量测定的代谢数据，以及1088个物种的环境本体生态数据，以此探究生态位广度的演化规律。研究发现，碳源利用广度的种间显著差异源自编码特定代谢通路的基因内在差异，未检测到进化权衡的证据，且外在生态因素的作用十分有限。本套全面的数据证实，内在因素驱动了微生物生态位广度的变异。
本数据集包含本项目中完成测序或重新注释的1154株出芽酵母菌的基因组序列与配套注释信息。
<strong>y1000p_cds_files.tar.gz</strong>：格式为assembly_fullID.final.cds的核苷酸序列Fasta文件，对应基因注释的编码区序列
<strong>y1000p_gff3_files.tar.gz</strong>：格式为assembly_fullID.final.gff3的GFF3格式基因注释文件
<strong>y1000p_gtf_files.tar.gz</strong>：格式为assembly_fullID.final.gtf的GTF格式基因注释文件
<strong>y1000p_pep_files.tar.gz</strong>：格式为assembly_fullID.final.pep的氨基酸序列Fasta文件，对应基因注释的蛋白序列
<strong>y1000p_genome_files.zip</strong>：格式为assembly_fullID.fas.gz的组装后基因组序列Fasta文件