@phdthesis{Derežanin2023,
  author    = {Derežanin, Lorena},
  title     = {Contribution of structural variation to adaptive evolution of mammalian genomes},
  doi       = {10.25932/publishup-59144},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-591443},
  school      = {Universit{\"a}t Potsdam},
  pages     = {188},
  year      = {2023},
  abstract  = {Following the extinction of dinosaurs, the great adaptive radiation of mammals occurred, giving rise to an astonishing ecological and phenotypic diversity of mammalian species. Even closely related species often inhabit vastly different habitats, where they encounter diverse environmental challenges and are exposed to different evolutionary pressures. As a response, mammals evolved various adaptive phenotypes over time, such as morphological, physiological and behavioural ones. Mammalian genomes vary in their content and structure and this variation represents the molecular mechanism for the long-term evolution of phenotypic variation. However, understanding this molecular basis of adaptive phenotypic variation is usually not straightforward. The recent development of sequencing technologies and bioinformatics tools has enabled a better insight into mammalian genomes. Through these advances, it was acknowledged that mammalian genomes differ more, both within and between species, as a consequence of structural variation compared to single-nucleotide differences. Structural variant types investigated in this thesis - such as deletion, duplication, inversion and insertion, represent a change in the structure of the genome, impacting the size, copy number, orientation and content of DNA sequences. Unlike short variants, structural variants can span multiple genes. They can alter gene dosage, and cause notable gene expression differences and subsequently phenotypic differences. Thus, they can lead to a more dramatic effect on the fitness (reproductive success) of individuals, local adaptation of populations and speciation. In this thesis, I investigated and evaluated the potential functional effect of structural variations on the genomes of mustelid species. To detect the genomic regions associated with phenotypic variation I assembled the first reference genome of the tayra (Eira barbara) relying on linked-read sequencing technology to achieve a high level of genome completeness important for reliable structural variant discovery. I then set up a bioinformatics pipeline to conduct a comparative genomic analysis and explore variation between mustelid species living in different environments. I found numerous genes associated with species-specific phenotypes related to diet, body condition and reproduction among others, to be impacted by structural variants. Furthermore, I investigated the effects of artificial selection on structural variants in mice selected for high fertility, increased body mass and high endurance. Through selective breeding of each mouse line, the desired phenotypes have spread within these populations, while maintaining structural variants specific to each line. In comparison to the control line, the litter size has doubled in the fertility lines, individuals in the high body mass lines have become considerably larger, and mice selected for treadmill performance covered substantially more distance. Structural variants were found in higher numbers in these trait-selected lines than in the control line when compared to the mouse reference genome. Moreover, we have found twice as many structural variants spanning protein-coding genes (specific to each line) in trait-selected lines. Several of these variants affect genes associated with selected phenotypic traits. These results imply that structural variation does indeed contribute to the evolution of the selected phenotypes and is heritable. Finally, I suggest a set of critical metrics of genomic data that should be considered for a stringent structural variation analysis as comparative genomic studies strongly rely on the contiguity and completeness of genome assemblies. Because most of the available data used to represent reference genomes of mammalian species is generated using short-read sequencing technologies, we may have incomplete knowledge of genomic features. Therefore, a cautious structural variation analysis is required to minimize the effect of technical constraints. The impact of structural variants on the adaptive evolution of mammalian genomes is slowly gaining more focus but it is still incorporated in only a small number of population studies. In my thesis, I advocate the inclusion of structural variants in studies of genomic diversity for a more comprehensive insight into genomic variation within and between species, and its effect on adaptive evolution.},
  language  = {en}
}
@phdthesis{Carrasco2023,
  author    = {Carrasco, Tomas},
  title     = {Genome structure analysis and patterns of transposable elements evolution in the slow-evolving Testudines clade},
  doi       = {10.25932/publishup-60657},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-606577},
  school      = {Universit{\"a}t Potsdam},
  pages     = {144},
  year      = {2023},
  abstract  = {Transposable elements (TEs) are loci that can replicate and multiply within the genome of their host. Within the host, TEs through transposition are responsible for variation on genomic architecture and gene regulation across all vertebrates. Genome assemblies have increased in numbers in recent years. However, to explore in deep the variations within different genomes, such as SNPs (single nucleotide polymorphism), INDELs (Insertion-deletion), satellites and transposable elements, we need high-quality genomes. Studies of molecular markers in the past 10 years have limitations to correlate with biological differences because molecular markers rely on the accuracy of the genomic resources. This has generated that a substantial part of the studies of TE in recent years have been on high quality genomic resources such as Drosophila, zebrafinch and maize. As testudine have a slow mutation rate lower only to crocodilians, with more than 300 species, adapted to different environments all across the globe, the testudine clade can help us to study variation. Here we propose Testudines as a clade to study variation and the abundance of TE on different species that diverged a long time ago. We investigated the genomic diversity of sea turtles, identifying key genomic regions associated to gene family duplication, specific expansion of particular TE families for Dermochelyidae and that are important for phenotypic differentiation, the impact of environmental changes on their populations, and the dynamics of TEs within different lineages. In chapter 1, we identify that despite high levels of genome synteny within sea turtles, we identified that regions of reduced collinearity and microchromosomes showed higher concentrations of multicopy gene families, as well as genetic distances between species, indicating their potential importance as sources of variation underlying phenotypic differentiation. We found that differences in the ecological niches occupied by leatherback and green turtles have led to contrasting evolutionary paths for their olfactory receptor genes. We identified in leatherback turtles a long-term low population size. Nonetheless, we identify no correlation between the regions of reduced collinearity with abundance of TEs or an accumulation of a particular TE group. In chapter 2, we identified that sea turtle genomes contain a significant proportion of TEs, with differences in TE abundance between species, and the discovery of a recent expansion of Penelope-like elements (PLEs) in the highly conserved sea turtle genome provides new insights into the dynamics of TEs within Testudines. In chapter 3, we compared the proportion of TE across the Testudine clade, and we identified that the proportion of transposable elements within the clade is stable, regardless of the quality of the assemblies. However, we identified that the proportion of TEs orders has correlation with genome quality depending of their expanded abundancy. For retrotransposon, a highly abundant element for this clade, we identify no correlation. However, for DNA elements a rarer element on this clade, correlate with the quality of the assemblies. Here we confirm that high-quality genomes are fundamental for the study of transposable element evolution and the conservation within the clade. The detection and abundance of specific orders of TEs are influenced by the quality of the genomes. We identified that a reduction in the population size on D. coriacea had left signals of long-term low population sizes on their genomes. On the same note we identified an expansion of TE on D. coriacea, not present in any other member of the available genomes of Testudines, strongly suggesting that it is a response of deregulation of TE on their genomes as consequences of the low population sizes. Here we have identified important genomic regions and gene families for phenotypic differentiation and highlighted the impact of environmental changes on the populations of sea turtles. We stated that accurate classification and analysis of TE families are important and require high-quality genome assemblies. Using TE analysis we manage to identify differences in highly syntenic species. These findings have significant implications for conservation and provide a foundation for further research into genome evolution and gene function in turtles and other vertebrates. Overall, this study contributes to our understanding of evolutionary change and adaptation mechanisms.},
  language  = {en}
}