Genomic convergence toward diploidy in Saccharomyces cerevisiae

Abstract

Genome size, a fundamental aspect of any organism, is subject to a variety of mutational and selection pressures. We investigated genome size evolution in haploid, diploid, and tetraploid initially isogenic lines of the yeast Saccharomyces cerevisiae. Over the course of approximately 1,800 generations of mitotic division, we observed convergence toward diploid DNA content in all replicate lines. This convergence was observed in both unstressful and stressful environments, although the rate of convergence was dependent on initial ploidy and evolutionary environment. Comparative genomic hybridization with microarrays revealed nearly euploid DNA content by the end of the experiment. As the vegetative life cycle of S. cerevisiae is predominantly diploid, this experiment provides evidence that genome size evolution is constrained, with selection favouring the genomic content typical of the yeast's evolutionary past.

Figure 1. A Snapshot of Genome Size Change across 1,766 Generations of Batch Culture Evolution

Each data point is the mean of three FACScan measurements on a single colony sampled from a population. Apparent fluctuations are largely a result of genome size polymorphisms, leading to sampling fluctuations depending on which colony was randomly chosen (see Figure S1). The average standard error (shown in panel A) reflects measurement error. FL1 represents a linear scale of dye fluorescence as measured by flow cytometry. The five lines on each graph represent the five replicate lines evolved independently.

Figure 2. The Three Indels Identified by CGH Analysis of Ancestral (Generation 0) and Evolved (Generation 1,766) Tetraploid Lines

(i) An insertion of a ~13-kilobase fragment on Chromosome 4 in tetraploid salt line qs; (ii) a potential ~36-kilobase deletion of Chromosome 5 in tetraploid line R; (iii) a potential 20-kilobase deletion of Chromosome 12 in tetraploid salt line rs. (A) Results of CGH, where each dot represents the mean (bars: 95% CI) relative copy number of all genes in the indel from a single array. (B) Genes of known function (http://www.yeastgenome.org 2 October 2005) affected by the indel (basepair range of genes involved are given in brackets). Each box is one ORF, where red indicates transcription on the Watson strand, and blue for genes transcribed on the Crick strand.

Figure 3. Rate of Genomic Size Change by Ploidy and Environment

Rate of change was calculated by fitting linear regression lines through timeseries data (Figure 1) for each individually evolved line. Each data point thus represents the mean ± SE of five slope measures. This figure shows that haploids increased in genome size faster in salt, while tetraploids decreased in genome size more slowly in salt.