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Karyotypic charachterization and population genomic analysis of the fungal grass pathogen Zymoseptoria ardabiliae

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Braker, I. (2017). Karyotypic charachterization and population genomic analysis of the fungal grass pathogen Zymoseptoria ardabiliae. Master Thesis, Christian-Albrechts-Universität zu Kiel, Kiel.

Cite as: https://hdl.handle.net/21.11116/0000-0001-5461-3
The Zymoseptoria species complex consists of the closely related species Z. tritici, Z. pseudotritici, Z. brevis and Z. ardabiliae (Stukenbrock et al., 2012a). While Z. tritici is a highly specialized endemic wheat pathogen (Stukenbrock et al., 2011), the three sister species were isolated from different uncultivated grasses in Iran (Stukenbrock et al., 2007; Quaedvlieg et al., 2011). This system of closely related pathogen species with different hosts from cultivated and non-cultivated environments provides a unique model to study underlying genetics of plant pathogens as well as speciation history and the underlying genetics of reproductive isolation (Quaedvlieg et al., 2011; Stukenbrock et al., 2012a, Stukenbrock, 2013; Poppe et al., 2015).
This Master thesis studies the wild grass pathogen Z. ardabiliae with population genomic methods and a karyotypic characterization to find patterns of selection and to further the understanding of the evolution of the Zymoseptoria species complex. The aims of this thesis are to investigate whether Z. ardabiliae shows a similar chromosome composition as Z. tritici with essential and dispensable chromosomes and to analyze which regions in the genome of Z. ardabiliae have been undergoing accelerated evolution or been under positive (diversifying) selection.
A Pulsed Field Gel Electrophoresis showed extensive numeral and size polymorphisms in the chromosomes of Z. ardabiliae. Also, it was possible to identify a dispensable chromosome in the reference species Za17. The dN/dS ratio revealed that some protein coding genes in Z. ardabiliae are under positive diversifying selection, but no potential effector candidate could be identified with this method. An additional analysis with Tajima’s D subsequently led to the identification of a possible effector candidate. Furthermore, Tajima’s D showed that genes of Z. ardabiliae potentially evolve under balancing selection or show signs of population substructuring. A genome-wide analysis of Tajima’s D showed evidence of a potential population size shrinkage or population substructure. The Fst analysis revealed no evidence of a recent genetic introgression between the sister species Z. ardabiliae and Z. tritici.