The unusual type of reproduction we study is not found in any of the classic model organisms that are the subject of most scientific research. We therefore had to established a number of invertebrate study systems and developed or optimize methods for laboratory rearing as well as generated genomic data and molecular tools that were previously unavailable.
The first part of the project is focused on mealybugs, small plant-feeding insects that can be easily maintained in the lab. The aim of this project is to understand the difference in behaviour of male chromosomes depending on what parent they were inherited from. We have generated extensive genomic and transcriptomic data for both species as well as data on epigenetic modifications associated with chromosomes of maternal and paternal origin. We show that in mealybug males chromosomes inherited from the father show reduced transcription compared to those inherited from the mother, although they are not completely silenced. We also show that DNA methylation is associated with gene expression and might contribute to the different chromosome behaviour in males and females. Finally we have investigated a chromosome that is able to escape paternal elimination in males. We have sequenced this chromosomes, and show that it carries a number of genes that are expressed during male meiosis and might play a role in its ability to avoid elimination.
In the second part of the project aims to better understand the mechanism by which sex is determined. Here we have primarily focused on fungus gnats, small flies with a complex system of chromosome behaviour. Two types of chromosomes are thought to potentially play a role in sex determination. The first is a chromosome that is present in 2 copies and only found in the germline of the flies, while it is eliminated from somatic cells (germline restricted chromosomes, GRCs). We have generated sequence data from soma versus germline tissue and where able to identify sequences belonging to the GRCs and shown that 1) the GRCs together are almost as big as the rest of the genome, 2) the two copies are diverged and likely sex-specific in their inheritance 3) the GRCs show sequence similarity with the genome of another clade (the gall midges) that also has PGE putting into question previous work on the evolutionary history of PGE in flies. We also generated sequence data to study the evolution of the X chromosome in fungus gnats. We used a phylogenomic approach and showed that the evolution of PGE within flies has been associated with an extensive increase in the proportion of the genome that is X-linked and this finding suggest a possible role for X-chromosome drive in the origin of this reproductive system. Finally PhD Baird has further investigated the X chromosome and specifically characterized a large inversion on the X that is associated with maternal sex determination. These results have allowed us to estimate the evolutionary age of the inversion and identified a number of candidate sex determination genes.
Finally we focuses on how paternal genome elimination affects the evolution of males and females at the level of the genome. First of all we have developed theory to generate testable predictions and show that we expect PGE generally to lead to the feminization of the genome, although it depends on the degree by which paternal genes are expressed in males. We have done analyses in each of our study systems to test these predictions: 1) We studied sex-biased gene evolution using a population genetic analysis in mealybugs and show that male-biased and unbiased genes are constrained in their rate of evolution compared to genes expressed primarily in females. 2) We have studied patterns of sex biased gene expression in fungus gnats and show clear differences in their distribution across different parts of the genome. 3) We have generate genome and transcription data for globular springtails - a system we recently established in the lab - and find differences in the patterns of sex-specific genes expression between autosomes and X chromosomes.
