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Kelsey Brock Tracking the Evolutionary History of Development Genes: Implications for the Diversification of Fruits and Flowers in the Brassicaceae and Cleomaceae by Kelsey Brock A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Plant Biology Department of Biological Sciences University of Alberta © Kelsey Brock, 2014 Abstract Flowers of Brassicaceae are remarkably similar across all species, whereas their fruits vary in almost all conceivable traits, particularly in the tribe Brassiceae. In contrast, Brassicaceae’s sister family, Cleomaceae, exhibits substantial variation in flowers but are more uniform in their fruits. These diversifications represent either variation in pollen transfer or seed dispersal, which are important reproductive traits that likely affect survival. The history of both families involves four shared polyploidy events as well as each independently experiencing separate additional polyploid events. Thus, these families offer an excellent opportunity to investigate whether additional genetic materials from polyploid events are correlated with the evolution of novel flower and fruit morphologies. Based on knowledge from model plants, FRUITFULL (FUL), a fruit development gene important for dehiscence (fruit opening), and TEOSINTE BRANCHED 1/ CYCLOIDEA/ PROLIFERATING CELL FACTOR 1 (TCP1), a gene known to affect floral symmetry, were chosen as candidate genes to examine the evolutionary history and retention of gene duplicates alongside morphological novelty in Brassicaceae and Cleomaceae. A gene phylogeny of FUL was generated to determine if fruit diversity in the tribe Brassiceae (Brassicaceae) could be correlated with FUL copy number, structure, or evolutionary history. Similarly, TCP1 was assessed to identify differences in gene evolutionary history between the florally diverse Cleomaceae and the florally uniform Brassicaceae. Both FUL and TCP1 were found to exhibit complex evolutionary histories, with multiple copies of these genes found in both taxa with and without morphological novelty. However, evaluation of which copies were retained and the rates of selection acting on these genes suggest their involvement in generating morphological diversity of reproductive ii structures. This thesis presents a strong correlative framework to direct future hypothesis testing using gene expression and functional approaches to further unravel the genetic changes underlying flower and fruit diversification. iii Acknowledgements I thank my supervisor Dr. Jocelyn Hall for her advice, enthusiasm, and for always showing optimism and unyielding support of my career goals. I would also like to thank Dr. Felix Sperling and Dr. Janice Cooke for offering a wealth of experience and ideas throughout the completion of this thesis. Additionally, I thank Dr. David Coltman for generously agreeing to be an arms-length examiner during the defense of my thesis. I thank Drs. Patrick Edger and J. Chris Pires for kindly providing access to the unpublished Cleome violacea genome and Dr. Suzanne Warwick for providing DNA of Brassica napus. I’d also like to thank the University of Alberta Molecular Biology Service Unit staff for their advice and assistance. I thank Dorothy Fabijan and Karen Romanyk for being an endlessly impressive source of information and for offering guidance during my teaching assistantships. My lab mates, Brittney Miller, Melanie Patchell, Mónica Higuera, Peter Mankowski, and Stephanie McCrea are thanked for their wisdom and humour. Lastly, I thank my parents Cheryl Langford-Brock and Dewey Brock and my husband, Jared Bernard, for their constant help, support and perspective. iv Table of Contents Abstract ..................................................................................................................................................................... ii Acknowledgements ............................................................................................................................................. iv List of Tables ......................................................................................................................................................... vii List of Figures ....................................................................................................................................................... vii Chapter 1 – Introduction ................................................................................................................................ 1 The diversity of angiosperms ...................................................................................................................... 1 Gene duplications as drivers of morphological diversity ................................................................. 2 A history of polyploidization and morphological novelty in two sister families..................... 4 The evolution of fruit ...................................................................................................................................... 6 The evolution floral symmetry ................................................................................................................... 8 Studying development genes in a phylogenetic context ................................................................ 12 Goals ................................................................................................................................................................... 14 References ........................................................................................................................................................ 15 Chapter 2 – FRUITFULL evolution in Brassiceae (Brassicaceae): insight into the diversification of fruit morphology ....................................................................................................... 26 Introduction ......................................................................................................................................................... 26 Methods............................................................................................................................................................. 32 Taxon sampling ............................................................................................................................................................. 32 Amplification, cloning and sequencing ............................................................................................................... 33 Sequence alignment .................................................................................................................................................... 36 Phylogenetic analysis ................................................................................................................................................. 37 Descriptive statistics .................................................................................................................................................. 38 Results ............................................................................................................................................................... 40 Statistics on the data sets ......................................................................................................................................... 40 Phylogenetic analyses ................................................................................................................................................ 40 Copy number and intron length ............................................................................................................................. 41 Selection tests ................................................................................................................................................................ 42 Discussion ........................................................................................................................................................ 44 Evolution and copy number of FUL in Brassiceae .......................................................................................... 44 Copy number and heteroarthrocarpy ................................................................................................................. 47 Gene structure and fruit morphology .................................................................................................................. 49 Molecular evolution models and longitudinal dehiscence ......................................................................... 50 v Conclusions..................................................................................................................................................................... 51 References ........................................................................................................................................................ 53 Tables ................................................................................................................................................................. 62 Figures ............................................................................................................................................................... 67 Chapter 3 – The Evolution of TCP1 genes in Brassicaceae and Cleomaceae: setting the stage for floral monosymmetry studies .............................................................................................
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