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Evolutionary Developmental Leaf Morphology of the Plant Family Araceae Claudia Liliana Henriquez Washington University in St

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Evolutionary Developmental Leaf Morphology of the Plant Family Araceae Claudia Liliana Henriquez Washington University in St Washington University in St. Louis Washington University Open Scholarship Arts & Sciences Electronic Theses and Dissertations Arts & Sciences Summer 8-15-2015 Evolutionary Developmental Leaf Morphology of the Plant Family Araceae Claudia Liliana Henriquez Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/art_sci_etds Part of the Biology Commons Recommended Citation Henriquez, Claudia Liliana, "Evolutionary Developmental Leaf Morphology of the Plant Family Araceae" (2015). Arts & Sciences Electronic Theses and Dissertations. 573. https://openscholarship.wustl.edu/art_sci_etds/573 This Dissertation is brought to you for free and open access by the Arts & Sciences at Washington University Open Scholarship. It has been accepted for inclusion in Arts & Sciences Electronic Theses and Dissertations by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Division of Biology and Biomedical Sciences Evolution, Ecology and Population Biology Dissertation Examination Committee: Allan Larson, Chair Thomas B. Croat Justin C. Fay Elizabeth A. Kellogg Kenneth M. Olsen Peter H. Raven Barbara A. Schaal Evolutionary Developmental Leaf Morphology of the Plant Family Araceae by Claudia Liliana Henriquez A dissertation presented to the Graduate School of Arts & Sciences of Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy August 2015 St. Louis, Missouri © 2015, Claudia Liliana Henriquez Table of Contents List of Figures................................................................................................................................. v List of Tables ................................................................................................................................ vii Acknowledgments ....................................................................................................................... viii Abstract of the Dissertation .......................................................................................................... xv Introduction of the Dissertation ...................................................................................................... 1 Chapter 1: Phylogenomics of the Plant Family Araceae ............................................................. 20 1.1 Introduction ...................................................................................................................... 28 1.2 Materials and Methods.................................................................................................... 32 1.2.1 Taxon Sampling..................................................................................................................... 32 1.2.2 Illumina sequencing............................................................................................................... 34 1.2.3 Data quality-trimming and filtering....................................................................................... 36 1.2.4 Sequence assembly, validation and alignment of chloroplast coding sequences.................. 38 1.2.5 Sequence assembly and alignment of the entire chloroplast ................................................. 39 1.2.6 Sequence assembly and alignment of mitochondrial sequences ........................................... 40 1.2.7 Phylogenomic analyses.......................................................................................................... 42 1.3 Results............................................................................................................................. 43 1.3.1 Phylogenomic analyses of chloroplast sequences ................................................................. 43 1.3.2 Comparison of chloroplast and mitochondrial phylogenies.................................................. 46 1.3.3 Synapomorphic indels in chloroplast protein-coding genes for major named taxa .............. 47 1.4 Discussion ....................................................................................................................... 48 1.4.1 Evolutionary relationships of Araceae .................................................................................. 48 1.4.2 Phylogenomics: chloroplasts vs. mitochondria .................................................................... 52 1.4.3 Problematic genes and Zantedeschia..................................................................................... 53 1.5 Conclusion....................................................................................................................... 54 1.6 References ....................................................................................................................... 56 Chapter 2: Development of Dissected Leaf Morphology In Anthurium and Amorphophallus .... 62 2.1 Introduction ...................................................................................................................... 63 2.2 Materials and Methods..................................................................................................... 68 2.2.1 Living and embedded plant material and species verification .............................................. 68 2.2.2 Scanning Electron Microscopy and Histology ...................................................................... 70 ii 2.3 Results.............................................................................................................................. 71 2.3.1 Phylogenetic position of species of Anthurium used in this study ........................................ 71 2.3.2 Leaf development in Anthurium ............................................................................................ 72 2.3.3 Leaf development in Amorphophallus................................................................................... 81 2.4 Discussion ........................................................................................................................ 85 2.4.1 Leaf types in Anthurium ........................................................................................................ 85 2.4.2 The role of adaxial-abaxial polarity genes ............................................................................ 86 2.4.3 The role of KNOX1 genes in dissected leaf development ..................................................... 88 2.5 References ........................................................................................................................ 89 Chapter 3: The Elusive Role of KNOX1 genes In Dissected Leaf Developmental In Anthurium and Amorphophallus..................................................................................................................... 94 3.1 Introduction ...................................................................................................................... 95 3.2 Materials and Methods.................................................................................................... 98 3.2.1 Living and embedded plant material ..................................................................................... 98 3.2.2 Western Blot Analysis........................................................................................................... 99 3.2.3 Immunolocalization............................................................................................................. 100 3.2.4 Class I KNOX gene characterization in Anthurium ............................................................. 102 3.2.5 RT-PCR ............................................................................................................................... 111 3.3 Results........................................................................................................................... 116 3.3.1 Western Blot........................................................................................................................ 116 3.3.2 Immunolocalization............................................................................................................. 118 3.3.3 Characterization of class I KNOX genes in Anthurium ....................................................... 121 3.3.4 RT-PCR ............................................................................................................................... 125 3.4 Discussion ..................................................................................................................... 128 3.5 References ..................................................................................................................... 130 Chapter 4: Leaf Development in Araceae: A New Look at the "Monocot Leaf vs. Dicot Leaf" Paradigm ..................................................................................................................................... 134 4.1 Introduction .................................................................................................................... 135 4.1.1 The Phyllode theory............................................................................................................. 135 4.1.2 The Leaf-base theory........................................................................................................... 136 4.1.3 Araceae, Alismatales and the Leaf-base theory................................................................... 137 4.1.4 The Transition-zone theory ................................................................................................
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