ausblenden:
Sprache(n):
eng - English
Datum:
2017-072017-07
Publikationsstatus:
Erschienen
Seiten:
73
Ort, Verlag, Ausgabe:
Kiel : Christian-Albrechts-Universität zu Kiel
Inhaltsverzeichnis:
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
Art der Begutachtung:
-
Identifikatoren:
Anderer: Dipl/12916
Art des Abschluß:
Master
