Genomics of Arbuscular Mycorrhizal Fungi : Expanding knowledge, one assembly at a time

Sammanfattning: Most life forms that inhabit Earth today are still unknown or are difficult to study. Accessing their DNA can give us information of their biology, ecology, and evolution, even when unculturable. The research here presented focused on method development for genomic research of non-model organisms. Paper I and II contributed to a comprehensive expansion of the genomic data available in arbuscular mycorrhizal (AM) fungi, an essential group of plant symbionts. While paper III and IV focused on the analysis of the generated genomic data. Paper I presents the development of a workflow that allows for DNA sequencing and assembling of AM fungal genomes, from as little as one single spore, by sorting and individually amplifying and sequencing nuclei. In paper II, the novel workflow was utilized to expand genomic data on AM fungi, by generating de novo genome assemblies from 22 different taxa. The evolutionary relationships within the group was also explored. In paper III possible genetic differences between nuclei of individual AM fungal organisms was examined, following the hypothesis of their sole reproductive asexual mode. Our results suggest low levels of genetic variation within the studied taxa. We also located genes involved in mating recognition, supporting earlier observations of a possible hitherto unknown sexual stage in AM fungal life cycle. Paper IV explores an important component that affects genomic architecture, the so-called transposable elements (TEs), which are selfish genetic elements that have the ability to move and multiply within the genome. These elements must be analyzed carefully, as we found that a significant part of what is initially classified as unknown repeat sequences are, in fact, not TEs, but genes from the fungus itself, that appear in many copies. We confirm that AM fungi contain a high proportion of TEs in their genomes. Furthermore, analyzing the evolutionary history of these genera, we observe a link with the existence of a possible control mechanism in the genus Rhizophagus. Our novel workflow and the comprehensive taxon sampling go beyond a few model organisms to bring the diverse monophyletic lineage of AM fungi fully into the genomic era.

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