Chromosome Level Genome Assemblies of Rhizophagus irregularis Strains Reveal Genome Evolution and Nuclear Structure in Arbuscular Mycorrhizal Fungi

Abstract

The quality of the available genome assemblies directly dictates the quality of thegenome analyses one can perform on a given species. If the aim is to study the mode of evolutionand to discover the genome biology of an organism, ideally chromosome level genomeassemblies are required to obtain the best results. Arbuscular mycorrhizal fungi (AMF) are oneof these organisms that suffered from the lack of high-quality reference genome assemblies,which hindered in-depth analyses performed on these organisms. Despite the lack of high-qualitygenome assemblies, AMF symbionts have been a research focus for many decades in fungalgenomics. These obligate symbionts colonize the roots of vascular plants and increase the overallroot uptake of their hosts with the help of their extended hyphae. AMF have a unique cellularbiology. Their cells are multinucleated with thousands of nuclei moving through their aseptatehyphae, and it was recently shown that depending on the strain, AMF nuclei either contain verysimilar genomic material (AMF homokaryons) or contain one of the two parental haplotypes thatcoexist in the same organism (AMF dikaryons, or AMF heterokaryons) in Rhizophagusirregularis, a model AMF species. It is hypothesized that a cryptic sexual life cycle betweenAMF homokaryons and dikaryons might be the driving factor behind the evolutionary success ofthese mutual symbionts.My research aims to construct high quality reference genome assemblies to study thegenome biology and mode of evolution of AMF strains. To achieve this, I build my thesis intothree chapters. In the first chapter, I propose parasexual and sexual events that might take placein AMF dikaryons which might contribute to increased genome variability. In the secondchapter, I present the first chromosomal level genome assemblies constructed for AMFhomokaryons and reveal a two-compartment genome structure in R. irregularis nuclei. In myiiithird and final chapter, I construct parental haplotypes of AMF dikaryons, reveal a nuclearstructure like that I identified in other AMF homokaryons, and compare the parental haplotypesto each other and to other AMF homokaryons. Overall, this study provides new referencegenome assemblies for AMF homokaryons and dikaryons and reveal their interactions on agenome level. Furthermore, it provides new insights into their nuclear structure, as well as theirgenome biology and evolution. These discoveries help us investigate the factors that drive theevolutionary and ecological success of these plant symbionts and help us understand whichpossible nuclear mechanisms generate increased genetic diversity in AMF isolates.