Phylogenomics and functional annotation of 530 non-Saccharomyces yeasts from winemaking environments reveals their Fermentome and Flavorome

Dataset to support manuscript with the same title. The submitted documents were obtained with the following procedures: For the genomes downloaded from SRA database (raw data; without assembled version available), assembly was performed using SPAdes Genome Assembler software v.3.15.4 (Bankevich et al. 2012), using default parameters. Following, the 661 assembled were annotated using AUGUSTUS software v.3.4.0 (Stanke and Morgenstern 2005), considering 16 different pre-trained models, chosen as belonging to the Ascomycota phyla (11) or the Basidiomycota phyla (5): Ascomycota – S. cerevisiae S288c, C. albicans, Meyerozyma (Candida) guilliermondii, C. tropicalis, Debaryomyces hansenii, Eremothecium gossypii, Kluyveromyces lactis, Lodderomyces elongisporus, Scheffersomyces (Pichia) stipitis, Schizosaccharomyces pombe, and Yarrowia lipolytica; Basidiomycota – Cryptococcus neoformans, Coprinus, Laccaria bicolor, Phanerochaete chrysosporium and Ustilago maydis. Results were manually reviewed to select the most robust annotation in terms of predicted coding genes. The potential coding regions reported by AUGUSTUS were extracted from the complete genomes to FASTA files.

本数据集用于支撑同标题研究论文的发表。本次提交的相关文件通过以下流程获取：针对从SRA数据库（Sequence Read Archive）下载的基因组（原始数据，无现成组装版本），使用SPAdes基因组组装软件（SPAdes Genome Assembler）v3.15.4（Bankevich等，2012）并采用默认参数完成组装。随后，针对661个组装完成的基因组，使用AUGUSTUS注释软件（AUGUSTUS software）v3.4.0（Stanke与Morgenstern，2005）进行基因注释，本次注释选用了16种预训练模型，均选自子囊菌门（Ascomycota，共11种）与担子菌门（Basidiomycota，共5种）的模式物种，具体如下：子囊菌门：酿酒酵母S288c（S. cerevisiae S288c）、白色念珠菌（C. albicans）、迈耶氏梅耶酵母（原迈耶氏假丝酵母）（Meyerozyma (Candida) guilliermondii）、热带假丝酵母（C. tropicalis）、汉逊德巴利酵母（Debaryomyces hansenii）、棉病埃雷霉菌（Eremothecium gossypii）、乳酸克鲁维酵母（Kluyveromyces lactis）、长孢洛德酵母（Lodderomyces elongisporus）、嗜木谢弗酵母（原嗜木毕赤酵母）（Scheffersomyces (Pichia) stipitis）、粟酒裂殖酵母（Schizosaccharomyces pombe）以及解脂耶氏酵母（Yarrowia lipolytica）；担子菌门：新型隐球菌（Cryptococcus neoformans）、鬼伞属（Coprinus）、双色蜡蘑（Laccaria bicolor）、黄孢原毛平革菌（Phanerochaete chrysosporium）以及玉米黑粉菌（Ustilago maydis）。研究人员通过人工审阅，基于预测编码基因的可靠性筛选出最优注释结果。将AUGUSTUS预测得到的潜在编码区从完整基因组中提取为FASTA格式文件。

搜集汇总

背景与挑战

背景概述

该数据集包含530个来自酿酒环境的非酿酒酵母基因组，通过系统基因组学和功能注释方法，揭示了这些酵母的发酵组和风味组特征。数据集提供了组装的基因组、注释文件、蛋白质组和功能注释结果，支持相关研究在发酵和生物信息学领域的应用。