Abstract
Improving feedstock is critical to facilitate the commercial utilization of algae, in particular in open pond systems where, due to the presence of competitors and pests, high algal growth rates and stress tolerance are beneficial. Here we raised laboratory cultures of the model alga Chlamydomonas reinhardtii under serial dilution to explore the potential of crop improvement using natural selection. The alga was evolved for 1,880 generations in liquid medium under continuous light (EL population). At the end of the experiment, EL cells had a growth rate that was 35% greater than the progenitor population (PL). The removal of acetate from the medium demonstrated that EL growth enhancement largely relied on efficient usage of this organic carbon source. Genome re-sequencing uncovered 1,937 polymorphic DNA regions in the EL population with 149 single nucleotide polymorphisms resulting in amino acid substitutions. Transcriptome analysis showed, in the EL population, significant up regulation of genes involved in protein synthesis, the cell cycle and cellular respiration, whereas the DNA repair pathway and photosynthesis were down regulated. Like other algae, EL cells accumulated neutral lipids under nitrogen depletion. Our work demonstrates transcriptome and genome-wide impacts of natural selection on algal cells and points to a useful strategy for strain improvement.
Highlights
Growing global human population size places significant demands on hydrocarbon resources [1]
Our results demonstrate that selection using a serial dilution regime can be used to substantially modify gene expression patterns in C. reinhardtii
In the case of the faster growing evolved light (EL) population, these cells can be manipulated to produce neutral lipids, which is of interest to industry (e.g., [55])
Summary
Growing global human population size places significant demands on hydrocarbon resources [1]. Absent access to sexual recombination to develop hybrids and public misgivings about cultivating genetically engineered algae in open ponds [8], an alternative approach to strain improvement is experimental evolution [9,10,11,12,13]. Unlike culture perturbations that focus on specific pathways such as the carbon-concentrating mechanism [15,16] or the response to sulfur deprivation [17], serial transfer of eukaryotes placed under selective regimes over hundreds of generations may open up a ‘‘Pandora’s box’’ of genetic variation within populations [18] This variation would be reflected in the accumulation of DNA mutations, gene expression changes, and epigenetic modification [19] that impact a variety of metabolic pathways [20]. We tested the utility of strain improvement vis-a-vis long-term selection [11,14,20] using as inoculum a single colony of the cell wall-deficient mutant C. reinhardtii strain CC-503 (cw mt+) that has a sequenced genome [21]
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