Population Genomics of Cercospora beticola Dissertation In fulfillment of the requirements for the degree of “Dr. rer. nat” of the Faculty of Mathematics and Natural Sciences at the Christian Albrechts University of Kiel. Submitted by Lizel Potgieter March 2021 1 First examiner: Prof. Dr. rer. nat Eva Holtgrewe Stukenbrock Second examiner: Prof. Dr. rer. Nat. Tal Dagan Third Examiner: Prof. Dr. Irene Barnes Date of oral examination: 13th of April 2021 2 Table of Contents Summary...............................................................................................................................................5 Zusammenfassung................................................................................................................................8 General Introduction...........................................................................................................................12 Introduction....................................................................................................................................12 Domestication Processes Affecting Fungal Pathogen Evolution...................................................13 Evolutionary Theory on the Effect of Domestication on Fungal Pathogens.................................17 Plant-Pathogen Interactions During Infection...............................................................................19 Genome Evolution in Fungal Plant Pathogens..............................................................................21 Description of Model System........................................................................................................28 Beta species...............................................................................................................................28 The Ascomycete Genus Cercospora.........................................................................................32 The Molecular Interaction of Cercospora beticola and its Beta Hosts.....................................33 Beta vulgaris and Cercospora beticola as a Model System......................................................37 Scope of the Thesis.............................................................................................................................38 Chapter 1: On variant discovery in genomes of fungal plant pathogens............................................41 Abstract..........................................................................................................................................42 Introduction....................................................................................................................................43 Method Overview..........................................................................................................................46 Results and Discussion..................................................................................................................48 Perspective.....................................................................................................................................52 Acknowledgements........................................................................................................................53 References......................................................................................................................................54 Supplementary Materials for Chapter 1.........................................................................................56 Supplementary Tables...............................................................................................................56 List of Supplementary Tables Available Online........................................................................56 Population Simulation...............................................................................................................57 Short Variant Calling.................................................................................................................58 Recovery of Accessory Regions................................................................................................59 References.................................................................................................................................60 Chapter 2: Population genomics of Cercospora beticola suggests that recent host domestication has not influenced genome evolution.......................................................................................................64 Abstract..........................................................................................................................................64 Introduction....................................................................................................................................65 Methods and Materials...................................................................................................................70 Sample Collection and Clone Correction..................................................................................70 Genome Sequencing.................................................................................................................72 Quality Analysis and Read Processing......................................................................................73 Analyses of Population Structure..............................................................................................73 Analyses of Population Differentiation.....................................................................................74 Results............................................................................................................................................76 Sample Collection and Clone Correction..................................................................................76 Genome Sequencing, Quality Analysis and Read Processing..................................................80 Detection of Population Structure.............................................................................................80 Regions Differentiation the C. beticola Isolates from the UK from the Isolates from Mainland Europe and North America.......................................................................................................96 Characterising the Region on Conting CM008504.1 Located at 1.2 Mb..................................98 Characterising the FST Outlier Region on Contigs CM008499.1 and CM008502.1.................99 Discussion....................................................................................................................................103 3 Genetic Diversity of C. beticola from Sea Beet in the UK.....................................................103 Does Location of Host Domestication Have a Clear Influence on Population Structure?.....105 What Differentiates the Isolates Found on Different Hosts and at Different Locations?.......108 Conclusions and Perspectives......................................................................................................111 References....................................................................................................................................113 Supplementary Materials.............................................................................................................120 Supplementary Tables.............................................................................................................120 Supplementary Figures...........................................................................................................149 Supplementary Materials for Protocols in the Laboratory......................................................157 Scripts......................................................................................................................................159 Chapter 3: Genome content of the Cercospora genus predicts host range.......................................168 Abstract........................................................................................................................................168 Introduction..................................................................................................................................169 Methods and Materials.................................................................................................................172 Description of Cercospora Genomes......................................................................................172 Analysis of CAZymes and Effectors.......................................................................................173 Gene Family Expansions and Contractions in Cercospora....................................................174 Whole Genome Synteny Between C. beticola and C. cf. flagellaris......................................174 Results..........................................................................................................................................175 PacBio Sequencing of C. zeina...............................................................................................175 Analysis of CAZymes and Effectors.......................................................................................175 Whole Genome Synteny Between C. beticola and C. cf. flagellaris......................................180 Discussion....................................................................................................................................183