Mechanisms and significance of genome size variation in rotifers

Despite an explosive increase of genomic information during the last ten years, the ultimate causes of genome size variation in eukaryotes are still controversial. At the core of this controversy is the puzzling genome size variation across eukaryotic taxa, which spans approximately five orders of magnitude. In this project we aim to investigate the mechanisms and significance of genome size variation at short evolutionary timescales, such as variation among closely related species, among populations, and among individuals within a population. Intrapopulation genome size variation can be a powerful test bed for analyzing the ultimate causes of genome size evolution, because it allows studying the effects of changes in genome size in a relatively homogeneous genomic background. Our model system is the facultative (a)sexual rotifer Brachionus plicatilis, a cryptic species complex consisting of at least 14 closely related species. Within this complex we will focus on the so-called `Austria`-lineage, which has undergone a 1.9-3.5 fold increase in genome size relative to its sister-species. Furthermore, we will study in detail the OHJ-population, a population from "Obere Halbjochlacke" (a small alkaline water body near Illmitz, Lower Austria) within the `Austria`-lineage, which exhibits a remarkable 25% (1.25 fold) variation in genome size. Specifically, we propose the following aims: (1) Elucidate the mechanisms of genome size variation by comparative genome sequencing (i) between the `Austria`-lineage and its sister species, (ii) among populations within the `Austria`-lineage, (iii) within the OHJ-population, (2) to experimentally determine how variation in genome size is maintained in the OHJ-population and inherited during sexual reproduction, and (3) to test assumptions and predictions of general hypotheses on genome size evolution using intrapopulation genome size variation of the OHJ-population. Specifically, we will address the following assumptions and predictions: (i) Genome size variation at the population level significantly covaries with cell size, body size and egg development time, (ii) Clones with large genome size accumulate deleterious mutations faster than clones with small genome size, and (iii) Clones with small genome size are favored by selection for maximum population growth rates under nutrient limitation. We expect that the proposed work will contribute new and general insights into the mechanisms and ultimate causes of genome size variation. Our model system B. plicatilis offers an exceptionally broad methodology, including population-level experiments across many generations owing to its short life cycle, which is unparalleled by most current model organisms in genome size evolution. In addition, the proposed project would contribute new genomic data on an important understudied invertebrate.

The genomes of most animals and plants contain much more DNA than required for organismic function. Genome sequencing projects of the last two decades have established that repetitive DNA, in particular transposons, account for the majority of additional DNA. This phenomenon of dispensable DNA is particularly obvious in species that display within- population variation in genome size. In this project, we conducted the first in-depth analysis of within-population genome size variation in a Eukaryote, the rotifer Brachionus asplanchnoidis. Using comparative genome sequencing we have shown that the B. asplanchnoidis genome contains > 44% repetitive DNA (mostly transposons). Individuals of the same population differed strongly in genome size, but they could interbreed and produce viable and fertile offspring, which were intermediate in genome size between their parents. Population mean genome size could be selected up or down, thus increasing or decreasing the proportion of dispensable DNA in the genome. We identified large genomic elements, which are shuffled during sexual production, and which are responsible for the genome size differences between individuals. We also tested several hypotheses regarding the consequences of such genome size variation, in particular, the idea that the sheer amount of DNA may affect an organisms phenotype, independent of its information content. Indeed, we found that individuals with larger genomes produced larger eggs, on average, and that offspring hatching from these eggs required slightly longer to complete their embryonic development. Individuals with extremely large genomes were also less competitive in experimental populations growing in a nutrient-limited environment. Moderate increases in genome size, however, were not disadvantageous according to our experiments, which indicates that natural selection alone cannot purge all of the dispensable DNA from genomes. Altogether, our results provide new insights into how populations or nascent species may acquire large differences in genome size within only few generations, and they contribute to a better understanding of the puzzling diversity of genome sizes across Eukaryotes.