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Genetic and Pathogenic Differences Between Microdochium Nivale and Microdochium Majus

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Genetic and Pathogenic Differences Between Microdochium Nivale and Microdochium Majus Genetic and Pathogenic Differences Between Microdochium nivale and Microdochium majus by Linda Elizabeth Jewell A Thesis Presented to The University of Guelph In partial fulfilment of requirements for the degree of Doctor of Philosophy in Environmental Science Guelph, Ontario, Canada © Linda Elizabeth Jewell, December, 2013 ABSTRACT GENETIC AND PATHOGENIC DIFFERENCES BETWEEN MICRODOCHIUM NIVALE AND MICRODOCHIUM MAJUS Linda Elizabeth Jewell Advisor: University of Guelph, 2013 Professor Tom Hsiang Microdochium nivale and M. majus are fungal plant pathogens that cause cool-temperature diseases on grasses and cereals. Nucleotide sequences of four genetic regions were compared between isolates of M. nivale and M. majus from Triticum aestivum (wheat) collected in North America and Europe and for isolates of M. nivale from turfgrasses from both continents. Draft genome sequences were assembled for two isolates of M. majus and two of M. nivale from wheat and one from turfgrass. Dendograms constructed from these data resolved isolates of M. majus into separate clades by geographic origin. Among M. nivale, isolates were instead resolved by host plant species. Amplification of repetitive regions of DNA from M. nivale isolates collected from two proximate locations across three years grouped isolates by year, rather than by location. The mating-type (MAT1) and associated flanking genes of Microdochium were identified using the genome sequencing data to investigate the potential for these pathogens to produce ascospores. In all of the Microdochium genomes, and in all isolates assessed by PCR, only the MAT1-2-1 gene was identified. However, unpaired, single-conidium-derived colonies of M. majus produced fertile perithecia in the lab. This finding contrasts with the cannonical requirements for sexual spore production among the Ascomycota. To further explore this, MAT1 and flanking gene sequences were identified in the genome sequences of six additional species from Xylariaceae, no homologs of known MAT1-1-1 genes were detected, suggesting that the control of sexual reproduction among the Xylariaceae may be differentally regulated relative to other Sordariomycete species. Detached leaves of T. aestivum and Poa pratensis (Kentucky bluegrass) were inoculated with either M. nivale or M. majus and were incubated at either 23 ºC or at 4 ºC to investigate the infection processes of these pathogens. Despite reported field host preferences, the two pathogens were equally virulent on both host plants at the temperatures investigated. The results presented here reveal genetic, but not pathogenic, differences between M. nivale and M. majus and further demonstrate that sub-populations may exist within the groups of these pathogens on different host plants. ACKNOWLEDGEMENTS Firstly, and most importantly, I would like to thank my advisor Dr. Tom Hsiang for accepting me into his lab and inviting me to participate in this exciting and multifaceted research project. I have sincerely appreciated the opportunity that he has given me to learn a very diverse set of skills. I am also very appreciative of the opportunities that he has given me to participate in engaging and inspiring conferences throughout my time as a student. I would also like to thank all of the members of my thesis, qualifying examination, and defense committees for their patience, guidance, and helpful suggestions at every stage of my project. Thanks are also extended to the administrative and support staff at the University of Guelph, especially in the School of Environmental Sciences, for helping to make my time here at the U of G run smoothly. I would also like to thank the numerous collaborators who provided me with some of the samples or materials that contributed to these analyses. I thank my friends and my family, especially my parents Bernice and Calvin and my brother Chris for their love and support through all of the long years that I have been in school. Thank you to all of my labmates, both past and current, for their friendship and help. I would especially like to thank Amy Shi for her help with research, for her amazing skills as a tour guide, and for her cat-wrangling abilities. Thank you Anne-Miet, for being a morning person; to Mihaela, for support and friendship; to Sarah, for being a vegetarian and a travel buddy; to Vince, for his help with bioinformatics; to Brady, for his help with RNA; to unbelievable undergrads Holly, Sara, and Craig, for their assistance in the lab and their and friendship; and to everyone else I have had the pleasure of working with, for their kindness and assistance. Finally, because everyone would be horrified if I left them out, thank you Jim and Luke for your skills as alarm clocks and as supervisors of all fridge-related endeavours. iv TABLE OF CONTENTS ACKNOWLEDGEMENTS ..................................................................................................... iv TABLE OF CONTENTS .......................................................................................................... v LIST OF TABLES ................................................................................................................... xi LIST OF FIGURES ............................................................................................................... xvi LIST OF APPENDICES ...................................................................................................... xxiii LIST OF ABBREVIATIONS AND ACRONYMS ............................................................ xxvi Chapter 1 General Introduction & Literature Review .............................................................. 1 1.1 Introduction ..................................................................................................................... 1 1.2 General information about Microdochuim nivale and M. majus .................................... 2 1.2.1 Disease Cycle ........................................................................................................... 4 1.2.2 Phylogenetic classification of M. nivale and M. majus ........................................... 5 1.3 Differences between M. majus and M. nivale ................................................................. 6 1.3.1 Morphological characteristics .................................................................................. 7 1.3.2 Pathogenic differences ............................................................................................. 7 1.3.3 Genetic differences .................................................................................................. 8 1.4 Sexual Reproduction ....................................................................................................... 9 1.4.1 Sexual reproduction in the Ascomycota .................................................................. 9 1.4.2 Sexual reproduction in Microdochium nivale and M. majus ................................. 11 1.5 Sequencing techniques and bioinformatics ................................................................... 12 1.5.1 DNA sequencing techniques .................................................................................. 12 1.5.2 RNA sequencing .................................................................................................... 14 1.6 Hypotheses and Objectives ........................................................................................... 16 v 1.7 References for Chapter 1 .............................................................................................. 18 Chapter 2 Phylogenetic Analyses ........................................................................................... 25 2.1 Introduction ................................................................................................................... 25 2.1.1 Fungal taxonomy and nomenclature ...................................................................... 25 2.1.2 Molecular phylogeny ............................................................................................. 26 2.1.3 Genes used for molecular phylogeny in fungi ....................................................... 27 2.1.4 Tree-building algorithms ....................................................................................... 28 2.1.5 Genetic differences between and within M. nivale and M. majus ......................... 30 2.1.6 Objectives .............................................................................................................. 32 2.2 Materials and Methods .................................................................................................. 33 2.2.1 Sample Collection .................................................................................................. 33 2.2.2 DNA extraction ...................................................................................................... 34 2.2.3 Primer design and selection................................................................................. 35 2.2.4 PCR protocols and sequencing .............................................................................. 36 2.2.5 Sequence alignments and trees .............................................................................. 37 2.2.6 Restriction Digests ................................................................................................. 38 2.3 Results ........................................................................................................................... 38 2.3.1 Primer testing and design ......................................................................................
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