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

Assembled genomes 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 – <i>S. cerevisiae S288c</i>, <i>C. albicans</i>, <i>Meyerozyma (Candida) guilliermondii</i>, <i>C. tropicalis</i>, <i>Debaryomyces hansenii</i>, <i>Eremothecium gossypii</i>, <i>Kluyveromyces lactis</i>, <i>Lodderomyces elongisporus</i>, <i>Scheffersomyces (Pichia) stipitis</i>, <i>Schizosaccharomyces pombe</i>, and <i>Yarrowia lipolytica</i>; Basidiomycota – <i>Cryptococcus neoformans</i>, <i>Coprinus</i>, <i>Laccaria bicolor</i>, <i>Phanerochaete chrysosporium</i> and <i>Ustilago maydis</i>. 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.

本研究使用AUGUSTUS软件v3.4.0（Stanke与Morgenstern，2005）对组装完成的基因组进行注释，共采用16种预训练模型，其中11种隶属于子囊菌门（Ascomycota），剩余5种隶属于担子菌门（Basidiomycota）：子囊菌门相关模型对应物种包括：酿酒酵母（*S. cerevisiae*）S288c、白色念珠菌（*C. albicans*）、吉氏梅耶酵母（原吉氏假丝酵母，*Meyerozyma (Candida) guilliermondii*）、热带假丝酵母（*C. tropicalis*）、汉逊德巴利酵母（*Debaryomyces hansenii*）、棉阿舒囊霉（*Eremothecium gossypii*）、乳酸克鲁维酵母（*Kluyveromyces lactis*）、长孢洛德酵母（*Lodderomyces elongisporus*）、树干毕赤酵母（*Scheffersomyces (Pichia) stipitis*，原归类于毕赤酵母属）、粟酒裂殖酵母（*Schizosaccharomyces pombe*）以及解脂耶氏酵母（*Yarrowia lipolytica*）；担子菌门相关模型对应物种包括：新生隐球菌（*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*）。研究人员通过人工复核，基于预测编码基因的稳健性筛选出最优注释结果，并将AUGUSTUS预测得到的潜在编码区从完整基因组中提取，保存为FASTA格式文件。