Department of Integrative Biology, Oregon State University, Corvallis.
Genome Biol Evol. 2020 Aug 1;12(8):1302-1312. doi: 10.1093/gbe/evaa121.
Experimental evolution allows the observation of change over time as laboratory populations evolve in response to novel, controlled environments. Microbial evolution experiments take advantage of cryopreservation to archive experimental populations in glycerol media, creating a frozen, living "fossil" record. Prior research with Escherichia coli has shown that cryopreservation conditions can affect cell viability and that allele frequencies across the genome can change in response to a freeze-thaw event. We expand on these observations by characterizing fitness and genomic consequences of multiple freeze-thaw cycles in diploid yeast populations. Our study system is a highly recombinant Saccharomyces cerevisiae population (SGRP-4X) that harbors standing genetic variation that cryopreservation may threaten. We also investigate the four parental isogenic strains crossed to create the SGRP-4X. We measure cell viability over five consecutive freeze-thaw cycles; whereas we find that viability increases over time in the evolved recombinant populations, we observe no such viability improvements in the parental strains. We also collect genome-wide sequence data from experimental populations initially, after one freeze-thaw, and after five freeze-thaw cycles. In the recombinant evolved populations, we find a region of significant allele frequency change on chromosome 15 containing the ALR1 gene. In the parental strains, we find little evidence for new mutations. We conclude that cryopreserving yeast populations with standing genetic variation may have both phenotypic and genomic consequences, though the same cryopreservation practices may have only small impacts on populations with little or no initial variation.
实验进化允许观察随着实验室种群在应对新的、受控制的环境时随时间发生的变化。微生物进化实验利用冷冻保存将实验种群保存在甘油培养基中，从而创建一个冷冻的、活的“化石”记录。先前对大肠杆菌的研究表明，冷冻保存条件会影响细胞活力，并且整个基因组的等位基因频率会因冷冻-解冻事件而发生变化。我们通过表征二倍体酵母种群中多次冷冻-解冻循环的适应性和基因组后果来扩展这些观察结果。我们的研究系统是一个高度重组的酿酒酵母种群（SGRP-4X），它具有冷冻保存可能威胁到的遗传变异。我们还研究了创建 SGRP-4X 的四个亲本同源菌株。我们在五个连续的冷冻-解冻循环中测量细胞活力；虽然我们发现进化后的重组种群的活力随时间增加，但在亲本菌株中没有观察到这种活力的提高。我们还从最初、一次冷冻-解冻和五次冷冻-解冻循环后的实验种群中收集全基因组序列数据。在重组进化种群中，我们在包含 ALR1 基因的第 15 号染色体上发现了一个等位基因频率发生显著变化的区域。在亲本菌株中，我们几乎没有发现新突变的证据。我们得出的结论是，冷冻保存具有遗传变异的酵母种群可能会产生表型和基因组后果，尽管相同的冷冻保存实践可能对初始变异较少或没有的种群只有很小的影响。
