MHC diversity and expression in a songbird : Temporal and transgenerational variation

The immune system is of central importance to clear-off pathogens in order to keep an organism healthy. In vertebrates, the Major Histocompatibility Complex (MHC) is a genomic region that holds key genes involved in adaptive immunity and in particular in the antigen presenting process. The presentation relies on MHC class I (MHC-I) and MHC class II (MHC-II) molecules that are encoded by MHC-I and MHC-II genes, respectively. In passerine birds (songbirds; order Passeriformes), high MHC-I and MHC-IIB diversity (i.e., number of MHC alleles in an individual) has been reported compared to other avian orders. Each MHC molecule can present a limited number of antigens, therefore high MHC diversity could potentially be an advantage for presenting various antigens from different pathogens. My aim was to gain a deeper understanding on what mechanisms have led to high MHC diversity in passerines, how much of this MHC diversity is expressed and whether it varies in time and across generation. In this thesis, I mainly focused on a particular passerine, the great reed warbler (GRW; Acrocephalus arundinaceus) for which high MHC diversity has been previously described. In chapter I, the MHC genomic region was characterized in the GRW and also in three additional passerine species from which long-read genome assemblies were available. The MHC region is extended in Passeriformes and the MHC diversity in the GRW has expanded through repeated and multiple gene duplication events of single and trios of MHC genes; these MHC paralogs are likely to have evolved under the birth-and death model process. In chapter II, I wanted to assess the correctness of the estimated haploid MHC diversity found in the GRW genome and to compare the resolution between the estimated diploid MHC diversity found with long- and short-read sequencing techniques. The haplotype resolution was improved using short-read amplicons and I found that two MHC-IIB scaffolds holding tandemly duplicated genes were most likel