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

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

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 Creators:
Braker, Ines, Author
Stukenbrock, Eva H.1, Referee           
Schulenburg, Hinrich, Referee
Affiliations:
1Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_2068284              

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 Abstract: 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.

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Language(s): eng - English
 Dates: 2017-072017-07
 Publication Status: Published in print
 Pages: 73
 Publishing info: Kiel : Christian-Albrechts-Universität zu Kiel
 Table of Contents: Index
1. Abstract ...................................................................................................................... 3
2. Introduction ................................................................................................................ 4
3. Objectives .................................................................................................................10
4. Material and Methods ...............................................................................................11
4.1. Zymoseptoria isolates ..............................................................................................11
4.2. Pulsed Field Gel Electrophoresis .............................................................................11
DNA preparation ............................................................................................................11
PFGE conditions ............................................................................................................12
Identifying numeral polymorphisms ................................................................................12
4.3. Assemblies, MGAs and nucleotide variant detection ...............................................13
Genome data .................................................................................................................13
SPAdes assemblies .......................................................................................................13
MGAs and nucleotide variant detection ..........................................................................14
4.4. Model of candidate genes under positive diversifying selection ...............................15
4.5. Identifying potential candidate effector genes ..........................................................15
4.6. Computation of Tajima’s D ......................................................................................16
4.7. Computation of Fst values .......................................................................................17
4.8. Statistics ..................................................................................................................17
5. Results ......................................................................................................................18
5.1. Z. ardabiliae chromosome composition is highly polymorphic ..................................18
5.2. New Illumina assemblies of Z. ardabiliae .................................................................20
5.3. Multiple Genome alignments and nucleotide polymorphisms ...................................22
MGA of 17 Z. ardabiliae strains ......................................................................................22
MGA of 17 Z. ardabiliae and 13 Z. tritici strains ..............................................................22
Distribution of nucleotide variants in unitigs of Z. ardabiliae ...........................................23
5.4. Potential effector candidates....................................................................................24
5.5. dN/dS ratio ..............................................................................................................24
Signs of positive diversifying selection in protein coding genes ......................................24
No effector candidates under positive diversifying selection ...........................................24
5.6. Tajima’s D ...............................................................................................................24
2
Genome-wide mean of Tajima’s D is positive .................................................................25
Gene-wide mean is significantly higher than genome-wide mean ..................................26
Identification of potential effector candidate with Tajima’s D ..........................................26
Fst revealed potential signs of introgression or conservation .........................................29
6. Discussion and Conclusion .....................................................................................31
6.1. Chromosome composition .......................................................................................31
Presence/absence polymorphisms and chromosome number .......................................31
Potential influence of populations on chromosome composition .....................................33
6.2. Assembly quality and comparison ...........................................................................34
6.3. Multiple Genome Alignment .....................................................................................35
Mitochondrial DNA .........................................................................................................35
Potential signal for unitigs of dispensable chromosomes ...............................................37
6.4. dN/dS ratio ..............................................................................................................37
Positive diversifying selection in the Zymoseptoria species complex ..............................37
Positive diversifying selection in effector candidates ......................................................39
6.5. Tajima’s D ...............................................................................................................39
Demography or population substructure ........................................................................39
Balancing selection or population substructure ..............................................................41
Identification of potential effector candidates ..................................................................43
Potential sign of a different evolutionary history in genomic sections .............................45
6.6. Fst ...........................................................................................................................46
6.7. Conclusion ...............................................................................................................49
6.8. Perspectives ............................................................................................................50
7. Acknowledgements ..................................................................................................51
8. Zusammenfassung ...................................................................................................52
9. References ................................................................................................................53
10. Supplement ...............................................................................................................59
 Rev. Type: -
 Identifiers: Other: Dipl/12916
 Degree: Master

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