1. A link between growth rate variability and post-zygotic reproductive isolation
Naomi Ziv, Mark Siegal and David Gresham
Center for Genomics and Systems Biology, New York University
In single-celled microbes, variation in cell growth rates has important implications for evolution. A fast-growing lineage will rapidly outcompete even slightly slower growing lineages. However, increased cellular variability might provide an advantage in the face of novel and fluctuating environments. We used a high-throughput microscopy assay, which enables simultaneous analysis of growth rates of tens of thousands of individuals, including clonal populations of distinct genotypes, to determine the extent of variation in growth in the budding yeast, Saccharomyces cerevisiae. We identified two strains that differ in growth-rate variance despite nearly identical mean growth rates, providing evidence that alleles controlling phenotypic variability segregate in yeast populations. Surprisingly, the strains are reproductively isolated resulting in only 1% spore viability when crossed. The distribution of viable cells per tetrad and its inheritance suggest viability does not depend on the genotype of the spore. Although the surviving spores segregate the difference in growth-rate variability of the parents, only crosses between strains with opposite variability phenotypes result in low spore viability. Using successive back-crossing and whole-genome sequencing, we discovered that the strains may differ in the position of a 120kb section of chromosome 8. We are currently investigating if the transposition is sufficient to explain the reproductive isolation and its implications for cell growth variability.
Top: Unprocessed and processed image of a single field.
Bottom: Images and growth profiles for two representative micro-colonies.
Measuring growth rate distributions using a
high-throughput microcolony growth assay
Individual yeast cells are distributed in glass-bottom 96-well plates and imaged every hour (Levy, et al., 2012, Ziv,et al., 2013). As the cells grow and divide, they form micro-colonies, consisting of the original single cell and its progeny. Growth parameters are calculated by analyzing the change in micro-colony area over time.
Natural isolates differ in growth rate variability
and are reproductively isolated
Distribution of spore viability seems to segregate
as a single locus
Starting with a backcrossed strain which exhibits low spore viability, surviving spores were backcrossed to the same parental strain. Left – distributions of the number of viable cells per tetrad for one direction of backcrossing strategy.
While phenotyping strains covering a wide range of
genetic backgrounds and ecological histories.
I identified strains that differ in the extent of growth rate variability despite almost identical mean growth rates (Ziv,et al., 2013), (above-left). Surprisingly, the two strains are reproductively isolated resulting in only 1% F2 viability. The number of viable cells per tetrad follows a Poisson distribution (above-right), consistent with the viability not depending on the genotype of the spore. Viable F2s still segregate growth rate heterogeneity (below-left). However any cross between low and high variability strains results in low spore viability.
7 haploid progenitors of the last generation backcross (from both backcrossing directions), along with the parental (Netherlands and Finland), F2-91, F2-164 and a pool of 170 viable F2 strains were sequenced.
Whole genome sequencing reveals potential
120kb transposition
A back-crossing strategy (below)
to isolate the loci determining
spore viability and potentially
growth rate heterogeneity.
References:
Levy, S., Ziv, N., & Siegal, M. (2012). Bet hedging in yeast by heterogeneous, age-correlated expression of a stress protectant. PLoS Biology, 10(5): e
Ziv, N., M. L. Siegal, and D. Gresham. (2013). Genetic and Non-Genetic Determinants of Cell-Growth Variation Assessed by High-Throughput Microscopy. Molecular Biology and Evolution, 30(12):
Whole genome sequencing revealed 57,018 unique Netherlands SNPs and 24,279 unique Finland SNPs. Backcrossed strains are enriched for the correct parental genome and parental strains have no evidence of large scale copy number variation. All strains that when backcrossed will have low spore viability contain two copies of a 120kb segment of chromosome 8 (doubled read depth), one from each parental genome (above). This is consistent with a transposition of this segment in one of the parental genomes.
I am currently investigating the position of this segment in the different strains and its role in growth rate variability and reproductive isolation.