ELUCIDATING MONILOPHYTE GENOMICS: HOW POLYPLOIDY, TRANSPOSABLE ELEMENTS, AND THE ALTERNATION OF INDEPENDENT GENERATIONS DRIVE FERN EVOLUTION By DANIEL BLAINE MARCHANT A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2018 © 2018 Daniel Blaine Marchant To Granddad ACKNOWLEDGMENTS I thank my advisors, Doug and Pam Soltis, for their endless support both inside and outside the lab. I couldn’t have wished for a better graduate experience. I thank Emily Sessa, Brad Barbazuk, Matias Kirst, Paul Wolf, and Zhonghua Chen for their insights. I thank my past academic mentors, Andreas Madlung, Betsy Kirkpatrick, and Virginia Walbot, for teaching me to think scientifically and I thank my past non-academic mentors, Dick Held, Adam Stein, Karen Masters, and my grandfather, for teaching me to think critically. I thank my family for their frequent visits and my friends for their frequent distractions. Finally, I thank my funding sources: the National Science Foundation, University of Florida Genetics Institute, Australian Academy of Science, Botanical Society of America, and Integrated Digitized Biocollections. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS ...............................................................................................................4 LIST OF TABLES ...........................................................................................................................7 LIST OF FIGURES .........................................................................................................................8 ABSTRACT ...................................................................................................................................10 CHAPTERS 1 INTRODUCTION ..................................................................................................................12 2 PATTERNS OF ABIOTIC NICHE SHIFTS IN ALLOPOLYPLOIDS RELATIVE TO THEIR PROGENITORS ........................................................................................................16 Background .............................................................................................................................16 Materials and Methods ...........................................................................................................20 Polyploid Selection and Locality Data Collection ..........................................................20 ENM Layers ....................................................................................................................21 Niche Overlap and Breadth .............................................................................................22 Statistical Analyses ..........................................................................................................23 Results.....................................................................................................................................24 Discussion ...............................................................................................................................26 3 GENOME EVOLUTION IN PLANTS ..................................................................................38 Background .............................................................................................................................38 Polyploidy ...............................................................................................................................39 Transposable Elements ...........................................................................................................43 Horizontal Gene Transfer .......................................................................................................45 Alternative Splicing ................................................................................................................47 Summary .................................................................................................................................48 4 FINALLY FERNS: INSIGHTS INTO THE FIRT HOMOSPOROUS FERN GENOME ....53 Background .............................................................................................................................53 Materials and Methods ...........................................................................................................57 Tissue Samples ................................................................................................................57 Library Construction and Sequencing .............................................................................58 Genome Assembly ...........................................................................................................59 Transcriptome Assembly .................................................................................................60 Polyploidy ........................................................................................................................61 Repeat Characterization ...................................................................................................63 Dating Repeat Insertion Events .......................................................................................65 5 Results and Discussion ...........................................................................................................65 Genome Sequencing and Assembly ................................................................................65 Transcriptome Sequencing and Assembly ......................................................................66 Polyploidy ........................................................................................................................67 Repeat Diversity ..............................................................................................................70 Summary .................................................................................................................................73 5 GENETIC SPECIFICITYAND EVOLUTION UNDERLYING THE ALTERNATION OF GENERATIONS IN LAND PLANTS .............................................................................84 Background .............................................................................................................................84 Methods ..................................................................................................................................87 Tissue Samples ................................................................................................................87 Library Construction .......................................................................................................88 Transcriptome Assembly .................................................................................................88 Comparative Transcriptomics .........................................................................................89 Gene Family Evolution ....................................................................................................90 Results.....................................................................................................................................91 Generation-Specific Patterns of Gene Expression ..........................................................91 Ceratopteris ..............................................................................................................91 Across Land Plants ...................................................................................................93 Gene Family Evolution Across Land Plants ...................................................................94 Discussion ...............................................................................................................................96 6 CONCLUSIONS ..................................................................................................................109 APPENDIX: SUPPLEMENTARY MATERIALS......................................................................112 LIST OF REFERENCES .............................................................................................................118 BIOGRAPHICAL SKETCH .......................................................................................................139 6 LIST OF TABLES Table page 2-1 Niche categorization of polyploids relative to their progenitors. ......................................33 4-1 Ceratopteris genome assembly statistics. ..........................................................................82 4-2 Ceratopteris repeat diversity and composition ..................................................................83 5-1 Gene family life stage specificity in a moss, fern, and conifer. .......................................108 A-1 Polyploid systems used in this study and the means by which their progenitors were identified. .........................................................................................................................114 A-2 Source information for gametophyte-sporophyte comparisons. ......................................116 A-3 Representative species and data source for ancestral gene family reconstructions. ........117 7 LIST OF FIGURES Figure page 2-1 Predicted niches and statistical differentiation of niche contraction in the polyploid complex, Cystopteris tennesseensis. ..................................................................................34 2-2