GENOME EVOLUTION IN MONOCOTS A Dissertation Presented to The Faculty of the Graduate School At the University of Missouri In Partial Fulfillment Of the Requirements for the Degree Doctor of Philosophy By Kate L. Hertweck Dr. J. Chris Pires, Dissertation Advisor JULY 2011 The undersigned, appointed by the dean of the Graduate School, have examined the dissertation entitled GENOME EVOLUTION IN MONOCOTS Presented by Kate L. Hertweck A candidate for the degree of Doctor of Philosophy And hereby certify that, in their opinion, it is worthy of acceptance. Dr. J. Chris Pires Dr. Lori Eggert Dr. Candace Galen Dr. Rose‐Marie Muzika ACKNOWLEDGEMENTS I am indebted to many people for their assistance during the course of my graduate education. I would not have derived such a keen understanding of the learning process without the tutelage of Dr. Sandi Abell. Members of the Pires lab provided prolific support in improving lab techniques, computational analysis, greenhouse maintenance, and writing support. Team Monocot, including Dr. Mike Kinney, Dr. Roxi Steele, and Erica Wheeler were particularly helpful, but other lab members working on Brassicaceae (Dr. Zhiyong Xiong, Dr. Maqsood Rehman, Pat Edger, Tatiana Arias, Dustin Mayfield) all provided vital support as well. I am also grateful for the support of a high school student, Cady Anderson, and an undergraduate, Tori Docktor, for their assistance in laboratory procedures. Many people, scientist and otherwise, helped with field collections: Dr. Travis Columbus, Hester Bell, Doug and Judy McGoon, Julie Ketner, Katy Klymus, and William Alexander. Many thanks to Barb Sonderman for taking care of my greenhouse collection of many odd plants brought back from the field. I obtained irreplacable intellectual support from my peers at MU: Katy Frederick‐Hudson, Corey Hudson, Ashley Siegel, Jen Holland, Dr. Elene Valdivia, and other members of our Think Tank. My perpetually patient and helpful committee included Dr. Candi Galen, Dr. Lori Eggert, and Dr. Rose‐Marie Muzika. Finally, I owe deep thanks and appreciation to my advisor, Dr. J. Chris Pires. I am very proud to be the Pires lab “burnt pancake.” ii TABLE OF CONTENTS Acknowledgements.................................................................................................................. ii List of Figures .......................................................................................................................... vi List of Tables........................................................................................................................... vii Abstract..................................................................................................................................viii Chapter 1 INTRODUCTION ....................................................................................................... 1 Literature Cited.................................................................................................................... 8 CHAPTER 2 Phylogenetics, divergence times, and diversification from three genomic partitions in monocots ........................................................................................................... 10 Abstract ........................................................................................................................... 10 Introduction....................................................................................................................... 11 Materials and Methods ..................................................................................................... 14 Taxon Sampling......................................................................................................................................14 DNA extraction, PCR, cloning, and sequencing......................................................................................14 PHYC phylogenetic analysis ...................................................................................................................16 Concatenated phylogenetic analysis .....................................................................................................16 Divergence times and diversification.....................................................................................................17 Results .............................................................................................................................. 19 PHYC analysis .........................................................................................................................................19 Combined eight gene data set and analyses .........................................................................................20 Divergence times and diversification.....................................................................................................22 Discussion.......................................................................................................................... 24 iii Acknowledgements ........................................................................................................... 29 Literature Cited.................................................................................................................. 30 CHAPTER 3 Systematics and evolution of life history traits and genome size in the Tradescantia alliance (Commelinaceae)................................................................................. 59 Abstract ............................................................................................................................. 59 Introduction....................................................................................................................... 60 Materials and Methods ..................................................................................................... 63 Taxon selection .....................................................................................................................................63 Molecular methods ...............................................................................................................................64 Sequence alignment and phylogenetic analysis ....................................................................................65 Genome size data ..................................................................................................................................65 Life history traits....................................................................................................................................66 Biogeography.........................................................................................................................................67 Character evolution ...............................................................................................................................67 Results ............................................................................................................................... 68 Phylogenetic inference ..........................................................................................................................68 Character evolution and biogeography .................................................................................................70 Discussion.......................................................................................................................... 71 Phylogenetic classification.....................................................................................................................71 Character evolution and biogeography .................................................................................................73 Limitations of data.................................................................................................................................74 Acknowledgements ........................................................................................................... 74 Literature Cited ................................................................................................................. 75 CHAPTER 4 Assembly of three genomic partitions from Illumina genome survey sequences 96 Abstract ............................................................................................................................. 96 Introduction....................................................................................................................... 97 Methods .......................................................................................................................... 101 iv Taxon selection....................................................................................................................................101 Illumina sequencing.............................................................................................................................102 Sequence assembly, annotation and analysis .....................................................................................103 Results ............................................................................................................................. 106 Reference tests in Poaceae..................................................................................................................106 Quality assessment of plastome assembly in Poaceae........................................................................107 mtDNA results in Poaceae ...................................................................................................................109