Periodic Reporting for period 3 - PGErepro (How to break Mendel’s laws? The role of sexual conflict in the evolution of unusual transmission genetics)
Reporting period: 2022-01-01 to 2023-06-30
Under Mendelian inheritance, individuals receive one set of chromosomes from each of their parents, and transmit one set of these chromosomes at random to their offspring. Yet, in thousands of animals Mendel's laws are broken and the transmission of maternal and paternal alleles becomes unequal. Why such non-Mendelian reproductive systems have evolved repeatedly across the tree of life remains unclear. In this project we study a variety of arthropod species to understand why, when and how the transmission of genes from one generation to the next deviate from Mendel’s laws. We mainly focus on species with Paternal Genome Elimination: Males transmit only those chromosomes they inherited from their mother to their offspring, while paternal chromosomes are excluded from sperm through meiotic drive. This remarkable reproductive strategy is widespread and has evolved repeatedly among arthropods. Yet very few studies have attempted to understand how this type of reproduction occurs. To redress this we investigate a number of key features of this type of reproduction. More specifically we investigate the mechanisms by which the chromosomes of males behave differently depending on which parent they were inherited from. We also investigate why and how some parts of the genome show different behaviour than others. For example in the clade of flies we study a large part of the genome is only found in the germline and eliminated from all somatic cells. And in one of the mealybug species we study one "parasitic" chromosome is able to escape the eliminated from sperm and can spread rapidly through populations despite reducing the fitness of its host. Finally we study how the sex of offspring is determined in species with Paternal Genome Elimination, as all species do not have conventional chromosomal sex determination. Together this work is generating new insights into the remarkable diversity by which organisms reproduce as well as the evolutionary forces that drive the diversification of these strategies. The work also provides insight into the biology of several economically important groups of invertebrates. Many species that reproduce through Paternal genome elimination are agricultural pest or parasites of humans and lifestock . A better understanding of their biology and genetics can help guide and design control strategies.
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.
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.
We developed an approach for identification of specific chromosomes by comparison of libraries decomposed to k-mers. This approach is relatively generic and we successfully used it to isolate germ-line restricted chromosomes and the sex determination locus of fungus gnats, and B chromosomes of the obscure mealybug. The apparent wide utility prompted us to organise a knowledge-exchange workshop based around this k-mer technique.