Studying Whole-Genome Duplication Using Experimental Evolution of Chlamydomonas

Abstract

In this chapter, we present the use of Chlamydomonas reinhardtii in experiments designed to study the evolutionary impacts of whole genome duplication. We shortly introduce the algal species and depict why it is an excellent model for experimental evolution. Subsequently, we discuss the most relevant steps and methods in the design of a ploidyrelated Chlamydomonas experiment. These steps include strain selection, ploidy determination, different methods of making diplo-and polyploid Chlamydomonas cells, replication, culturing conditions, preservation, and the ways to quantify phenotypic and genotypic change.

The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil

“…Evolution experiments with real biological organisms might be another means to get further insights into the mechanistic underpinnings explaining why duplicated GRNs might confer a selective advantage for polyploids during stressful times. By “replaying the duplication tape of life”, fitness of nonpolyploid and polyploid species can be evaluated under normal and stressful conditions ( 24 , 73 – 76 ). Transcriptomes can be sequenced, and phenotypic and physiological responses measured and linked to the duplication of genomes and GRNs.…”

Studying Whole-Genome Duplication Using Experimental Evolution of Spirodela polyrhiza

“…When the number of cells used for RNA extraction is known (e.g., single-celled organisms [4]), gene expression can be normalized per cell by adding heterologous RNA (e.g., External RNA Controls Consortium RNA) proportional to the cell number and looking at the expression of the gene of interest relative to the proportion of exogenous RNA. If the RNA is extracted from an unknown number of cells, which will be the case for Spirodela, the (relative) transcriptome size must be quantified.…”

“…The quantification of genetic change in the context of experimental evolution and, in particular, evolve and resequence experiments has been discussed in detail elsewhere in this issue [4].…”

“…The second comparison is limited by a restricted time frame that is generally too short to make inferences about evolution. This last problem is not imposed by the method itself but by the rather lengthy generation time of plants, and its solution lies in the use of organisms with a less constraining generation time such as the unicellular eukaryotes Saccharomyces cerevisiae (yeast) and Chlamydomonas reinhardtii (unicellular green alga) which have both been used to compare the evolution of ploidy variants (see also chapter by Bafort et al in this issue [4]).…”