Genome in equilibrium: Subgenome expression bias in allotetraploid common carp

The main aim of this thesis was to add to the fundamental understanding of polyploid animal genomes by using common carp (Cyprinus carpio) as an animal model. This thesis focused on whether both subgenomes have been retained in common carp through sharing functions between subgenome A and B, or through functional specialization of either subgenome.In chapter I, I first studied the duplicated regions within common carp by making a complete genome and identifying its subgenomes A and B. To study subgenome expression, I looked at induced gene expression of duplicated genes (ohnologs) shared between subgenome A and B. To this end I used genes part of a conserved immune gene network, known as interferon stimulated genes (ISGs). Both subgenomes symmetrically contribute in terms of expression of ohnolog genes before and after the immune challenge. These results point towards equal functional importance of subgenome A and B within this immune gene network and immune response. Chapter III addresses whether the symmetrically-distributed subgenome bias, observed in chapter II, was a consistent pattern across different tissues in common carp. I observed consistent subgenome expression bias towards both subgenomes A, or B, while the number of ohnologs with subgenome expression bias differed greatly between tissues. These findings hint at an evolutionary process of both, ohnolog retention through symmetric co-expression and tissue-specific specialisation. The subgenomes were also remarkably consistent in the number of ohnologs that had differential chromatin access. Though I found a positive correlation between chromatin accessibility and gene expression, this correlation could not explain the observed divergent subgenome expression bias patterns. Chapter IV addressed whether the observed subgenome expression bias in common carp would change after immune challenges of two different pathogen mimics, and thus if subgenome bias patterns can be changed by environmental stressors. I also focussed on chromatin access changes after the two immune challenges to see whether chromatin accessibility has a regulatory effect on changes in subgenome bias induced by a environmental stressor. The majority of ohnologs did not change their subgenome bias state, but we did observe differences in the degree of induction between ohnolog pairs. These asymmetrically induced ohnologs were equally divided between subgenome A and B, supporting the findings in chapter II of symmetrical functional division between the subgenomes. Combined, this expression analysis shows that ohnologs are co-induced to express symmetrically upon immune induction or show expression specialisation with one ohnolog, that can equally be from either subgenome, differentially expressing. Both immune challenges resulted in increased chromatin accessibility. I could not correlate this increase in accessibility with the observed differential expression changes after induction of both immune challenges, nor with the subgenome expression bias shifts. This PhD thesis demonstrates the importance of studying both subgenomes and their duplicated genes to fully understand biological function in a polyploid. I suggest that there is no clear subgenome dominance of one subgenome in common carp. Subgenome A and B are maintaining their duplicated genes though balanced expression, where most are co-expressing with or without subgenome bias.