Supplemental Material for Klim et al., 2018

p { margin-bottom: 0.21cm; direction: ltr; color: rgb(0, 0, 10); line-height: 115%; text-align: left; }p.western { font-family: "Calibri", serif; font-size: 11pt; }p.cjk { font-family: "Calibri"; font-size: 11pt; }p.ctl { font-family: "Arial"; font-size: 11pt; }a:link { color: rgb(0, 0, 255); text-decoration: none; } <b>Additional file 1.</b> Final alignments (files with .aln.fasta extension) and phylogenetic trees (files with fastree.newick extension) for all the protein families analyzed in the study. Additionally, in case of three protein families: AIF, OMI and caspase/metacaspase the subfolders were created, containing the key subtrees (files in nexml format generated with Dendroscope). <br> <b>Additional file 2</b><b>.</b> Additional BLASTP results and taxonomy reports conducted to confirm the key results in case of the three protein families: AIF, caspase/metacaspase and htra. BLASTP results and taxonomy reports were obtained with NCBI WWW with two strategies: by selecting only a few eukaryotic proteomes (for the species from Table S2 in Supplementary Methods) as a search database (see file eukaryotic_strategy.pdf) and by extending selected proteomes from the first search strategy with all bacterial and archeal proteomes (see file extended_strategy.pdf). Please see README.md for more details regarding information for given specific file. <br> <b>Additional file 3. </b>Mega sessions for consensus phylogenetic trees calculated for arbitrarily chosen metacaspases and caspases, OMI/HTRA proteases and AIFs. Separate sessions files are available for calculations based on MLE (maximum likelihood estimation), NJ (neighbor-joining) and ME (minimal evolution). <br> <b>Additional Figure S1.</b> Competition assay between <i>ndi1</i><i>Δ </i>and wild-type Saccharomyces cerevisiae BY4741 strains under anaerobic conditions. <br> <b>Additional Figure S2.</b> Growth curves for all tested in this study yeast strains cultivated in prolonged cultures in aerobic (A) or anaerobic (B) conditions. The values of mean and standard deviation from duplicate experiments are shown for each time point. <br> <b>Additional Figure S3. </b>Yeast strains used in the experimental evolution are unable to grow on medium supplemented with non-fermentable carbon source. Cells grown on glucose-containing (A) and glycerol-containing (B) solid medium. Single colonies were streaked on the appropriate plate and incubated at 28⁰C for 3 days. Wild-type strain shows robust growth on both media, whereas mutant strains grow only on glucose-containing plate.<br> <br>

<b>附加文件1</b>：本研究中分析的所有蛋白质家族的最终比对文件（扩展名为.aln.fasta）和系统发育树文件（扩展名为fastree.newick）。此外，针对AIF、OMI和caspase/metacaspase这三个蛋白质家族，我们创建了子文件夹，其中包含关键子树文件（采用Dendroscope生成的nexml格式文件）。<br><b>附加文件2</b>：针对AIF、caspase/metacaspase和htra三个蛋白质家族，为验证关键结果所开展的额外BLASTP比对结果与分类学报告。本次BLASTP比对结果及分类学报告通过NCBI网页端获取，采用两种策略：一是仅选取少量真核生物蛋白质组（即补充方法中表S2所列物种的蛋白质组）作为搜索数据库（对应文件"eukaryotic_strategy.pdf"）；二是在第一种策略的基础上，追加所有细菌和古菌蛋白质组作为搜索数据库（对应文件"extended_strategy.pdf"）。有关各文件的详细说明，请参阅README.md。<br><b>附加文件3</b>：针对随机选取的metacaspases与caspases、OMI/HTRA蛋白酶及AIFs，用于构建共识系统发育树的Mega会话文件。基于MLE（最大似然估计，maximum likelihood estimation）、NJ（邻接法，neighbor-joining）和ME（最小进化法，minimal evolution）三种方法的分析均提供了独立的会话文件。<br><b>附加图S1</b>：厌氧条件下ndi1Δ与野生型酿酒酵母(Saccharomyces cerevisiae) BY4741菌株的竞争实验。<br><b>附加图S2</b>：本研究中所有测试酵母菌株在有氧（A）或厌氧（B）条件下长期培养的生长曲线。每个时间点均展示了重复实验的平均值与标准差。<br><b>附加图S3</b>：本实验进化中使用的酵母菌株无法在以非发酵碳源为补充的培养基上生长。分别展示了在葡萄糖培养基（A）和甘油培养基（B）固体平板上的生长情况：将单菌落划线接种至对应平板，于28℃培养3天。野生型菌株在两种培养基上均能旺盛生长，而突变菌株仅能在葡萄糖培养基上生长。<br><br>