Chromosome evolution in Rhabditina (Nematoda) with a focus on programmed DNA elimination
Recent advances in DNA sequencing technologies have enabled research on the mechanisms that shape chromosome evolution in diverse taxa. My thesis focuses on nematodes from the Rhabditina suborder, which exhibit a high rate of chromosome rearrangement and have several species with chromosome-level assemblies available for comparison. To study chromosome evolution in this group, I inferred a set of loci that comprised the ancestral linkage groups, called Nigon elements, in rhabditid nematodes. This showed that the sex chromosome of the model nematode Caenorhabditis elegans is the product of a fusion of an ancestral autosome and the ancestral sex chromosome. As part of this work, I also generated the first telomere-to-telomere genome with no gaps of unknown sequence of a non-Caenorhabditis nematode, Oscheius tipulae. We serendipitously discovered that O. tipulae undergoes programmed DNA elimination (PDE) by identifying that both ends of each chromosome had two alternative terminal telomere repeat arrays. PDE is a developmentally controlled process whereby somatic cells selectively lose part of their genome. In total, less than 0.5% of the 60 Mb O. tipulae genome is eliminated. To gain insights into the evolution of PDE, I generated chromosome-level assemblies for four Oscheius species that are closely related to O. tipulae. These revealed PDE in all species, and linked PDE with variations in telomere length and breakage-associated sequence motifs. I characterised a novel gene family linked to chromosome ends, derived from helitron2-like transposable elements, and variably eliminated regions in Oscheius dolichura involving divergent paralogs of conserved genes. To facilitate comparative research, I propose a framework outlining a standard set of features for future studies. Finally, I applied this framework to characterise PDE in Auanema rhodensis, a species closely related to Oscheius in which over 60% of its genome is eliminated by PDE. The eliminated regions in A. rhodensis are also delineated by a sequence motif, contain protein-coding genes, ncRNAs, and share the same large tandem repeats between all autosomes. Together, my research sheds light on the evolution of nematode chromosomes and PDE.
Chromosome Evolution, Programmed DNA elimination, Chromatin Diminution, Telomere, Genome, Ancestral Linkage Groups, Nigon elements, Nematoda, Rhabditina, Oscheius
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