Table S7 from Rapid functional and evolutionary changes follow gene duplication in yeast

Duplication of genes or genomes provides the raw material for evolutionary innovation. After duplication a gene may be lost, recombine with another gene, have its function modified, or be retained in an unaltered state. The fate of duplication is usually studied by comparing extant genomes and reconstructing the most likely ancestral states. Valuable as this approach is, it may miss the most rapid evolutionary events. Here, we engineered strains of <i>Saccharomyces cerevisiae</i> carrying tandem and non-tandem duplications of the singleton gene <i>IFA38</i> to monitor (i) the fate of the duplicates in different conditions, including timescale and asymmetry of gene loss and (ii) the changes in fitness and transcriptome of the strains immediately after duplication and after experimental evolution. We found that the duplication brings widespread transcriptional changes but a fitness advantage is only present in fermentable media. In respiratory conditions, the yeast strains consistently lose the non-tandem <i>IFA38</i> gene copy in a surprisingly short time, within only few generations. This gene loss appears to be asymmetric and dependent on genome location since the original <i>IFA38</i> copy and the tandem duplicate are retained. Overall, this work shows for the first time that gene loss can be extremely rapid and context dependent.

基因或基因组重复为进化创新提供了原始素材。基因发生重复后，可能会丢失、与其他基因发生重组、功能发生改变，或是以未发生变异的状态被保留下来。目前针对重复事件命运的研究，通常通过比较现存基因组并重构最可能的祖先状态来开展。尽管该方法颇具价值，但却可能遗漏发生最为迅速的进化事件。本研究中，我们对酿酒酵母(Saccharomyces cerevisiae)菌株进行基因工程改造，使其携带单拷贝基因IFA38的串联重复与非串联重复拷贝，以此监测两个核心内容：(i) 不同培养条件下重复基因的命运，包括基因丢失的时间尺度与不对称性；(ii) 基因重复后即刻以及实验进化后，菌株的适合度与转录组变化。研究发现，基因重复会引发广泛的转录组变化，但仅在可发酵培养基中，菌株才会获得适合度优势。在呼吸型培养条件下，酵母菌株会在极短的数代繁殖内，持续丢失非串联型IFA38基因拷贝。该基因丢失过程呈现出不对称性，且受基因组位置影响——因为原始IFA38拷贝与串联重复拷贝均被保留了下来。总体而言，本研究首次证实，基因丢失的过程可以极为迅速，且具有环境依赖性。