Zeynep Akdeniz: Sequencing and comparative analyses of diplomonad genomes: Beyond the Gut: The Lake of Forgotten Dreams

Abstract

This thesis presents a comprehensive analysis of diplomonad genomes, focusing on both parasitic and free-living species, to explore the evolutionary adaptations within this group of anaerobic, flagellated eukaryotes. I first generated and analyzed the reference genome of Hexamita inflata, the first free-living diplomonad to be sequenced. The genome of H. inflata is significantly larger than those of parasitic diplomonads, with 142 Mbp encoding 79,341 proteins. The expansion of protein-encoding capacity and a high proportion of interspersed repeats contribute to the large genome size, providing a foundation for future studies on the evolution of parasitism and free-living lifestyles in diplomonads.

In a subsequent study, I improved the genome assembly of Spironucleus salmonicida, a diplomonad responsible for systemic infections in salmon, using PacBio long-read sequencing and optical mapping. The new assembly consolidates the genome into nine near-complete chromosomes, providing a more comprehensive view of the gene families, gene organization, and chromosomal structure. This high-quality reference genome will facilitate comparative genomic studies at the chromosomal level and serve as a valuable resource for researchers studying diplomonads and other protists.

Further, I generated the draft genome of the commensal diplomonad Spironucleus barkhanus, revealing a genome size (26.9 Mbp) larger than the morphologically similar S. salmonicida due to extensive duplications, expansions in protein-coding capacity, and a higher content of interspersed repeats. Comparative analysis between these two diplomonads highlighted key genomic differences, which are likely related to their distinct lifestyles. The S. barkhanus genome will contribute to understanding the pathogenicity of S. salmonicida and aid in the development of diagnostic tools to differentiate between these species in salmonid fish.

Finally, I performed a comparative genomic analysis using the GenoDiplo and CompareDiplo bioinformatics pipelines across various diplomonads with different lifestyles, revealing significant expansions in seven key protein superfamilies. The data suggest that environmental factors drive the evolution of these protein and multi-gene families, resulting in organisms that are well-adapted to their specific habitats. This work enhances our understanding of the diversity and evolutionary history of eukaryotes, particularly the adaptations to anaerobic lifestyles and the evolution of key eukaryotic cellular mechanisms.