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The Pennsylvania State University the Graduate School the Huck The Pennsylvania State University The Graduate School The Huck Institutes of the Life Sciences COMPARATIVE TRANSCRIPTOME AND PHYLOGENOMIC ANALYSES ON THE EVOLUTION OF PARASITIC OROBANCHACEAE A Dissertation in Plant Biology by Zhenzhen Yang © 2016 Zhenzhen Yang Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2016 The dissertation of Zhenzhen Yang was reviewed and approved* by the following: Claude W. dePamphilis Professor of Biology Dissertation Advisor Chair of Committee Charles T. Anderson Assistant Professor of Biology Naomi S. Altman Professor of Statistics Yinong Yang Associate Professor of Plant Pathology and Environmental Microbiology Teh-hui Kao Distinguished Professor of Biochemistry and Molecular Biology Chair of the Plant Biology Graduate Program *Signatures are on file in the Graduate School ii ABSTRACT Parasitic plants are plants that form a parasitic association with their host using a connecting organ called the haustorium, a novel feeding structure through which parasites withdraw nutrients such as carbon and nitrogen from the conducting tissues of the host. Orobanchaceae is the only family containing species with the full spectrum of parasitic capabilities, including one nonparasitic autotrophic genus, Lindenbergia, and more than 90 genera (>2000 species) of parasites with varying degrees of photosynthesis and host dependence. To understand the genetic changes that led to a parasitic lifestyle, a transcriptome sequencing project was initialized to interrogate multiple stages of growth and development of three parasitic plants that span the range of parasitic dependence. Around 180 genes are upregulated during haustorial development following host attachment in at least two species, and these are enriched in proteases, cell wall modifying enzymes, and extracellular secretion proteins. The majority of parasitism genes were duplicated before the divergence of Orobanchaceae and Mimulus, a related nonparasitic plant. This suggests that gene duplication plays a role in the origin of parasitism. A comparative analysis of these genes’ homologs in sequenced nonparasitic plant genomes revealed that parasitic plants make haustoria by co-opting genes from root and floral development. Gene duplication, often taking place in a nonparasitic ancestor of Orobanchaceae, followed by regulatory neofunctionalization, was an important process in the origin of parasitic haustoria. Horizontal gene transfer (HGT), acts as another evolutionary force contributing to parasite adaptation. At least 42 gene families accounting for 52 transfers – largely via genomic integration - result in functional transcripts that were primarily involved in translation, defense responses, transposable element (TE), and other diverse roles. Three lines of evidence indicate an adaptive role of HGT in parasite evolution - (i) A majority of HGT genes are upregulated in haustoria- related tissues in the most parasitic Phelipanche aegyptiaca; (ii) A higher frequency of HGTs are observed in parasites with a higher degree of parasitism; (iii) A portion of genes detected to have evolved some adaptive sites under positive selection. The study of strigolactone (SL) pathway in parasitic plants reveals that parasitic plants still retain genes in SL synthesis. Two SL biosynthesis genes and D14 (the receptor) are upregulated in haustorial structures, indicating a possibility of SL in haustoria development. iii TABLE OF CONTENTS LIST OF FIGURES ................................................................................................................. viii LIST OF TABLES ................................................................................................................... x ACKNOWLEDGEMENTS ..................................................................................................... xi Chapter 1 Introduction to parasitic plants and related research .............................................. 1 1.1 Introduction to parasitic plants .................................................................................... 2 1.1.1 Parasitic plants – classification and morphology ............................................ 2 1.1.2 Parasitic Orobanchaceae ................................................................................. 3 1.2 Biology of parasitic plants .......................................................................................... 3 1.2.1 Germination of parasitic plants ....................................................................... 3 1.2.2 The haustorium ................................................................................................ 4 1.2.3 Haustorium initiation and early development ................................................. 4 1.2.4 Haustorium penetration and development ....................................................... 5 1.2.5 Physiology of parasitic plants ......................................................................... 6 1.2.6 Nutrient transfer .............................................................................................. 7 1.3 Parasite control ............................................................................................................ 8 1.3.1 Problems and germination-based approaches ................................................. 8 1.3.2 Known parasitism genes .................................................................................. 9 1.3.3 Parasite and host defense – the arms race ....................................................... 10 1.4 Evolution of novel traits .............................................................................................. 12 1.4.1 Haustorium as a good model to study the evolution of novel traits ................ 12 1.4.2 Mechanisms for the origin of novel traits ....................................................... 12 1.4.3 Gene duplication and regulatory networks (origin of flower) ......................... 13 1.4.4 Homeobox domain-mediated regulation of leaf development ........................ 14 1.4.5 Co-option of existing genes and gene family expansion ................................. 14 1.4.6 Mutation-driven positive selection .................................................................. 15 1.4.7 Haustoria origins – the exogenous model (HGT) ........................................... 15 1.4.8 Haustoria origins – the endogenous model (gene recruitment) ....................... 17 1.5 Horizontal gene transfer .............................................................................................. 18 1.5.1 Mitochondrial HGT ......................................................................................... 18 1.5.2 HGT in parasitic plants ................................................................................... 19 1.5.3 HGT of non-plant origin ................................................................................. 20 1.5.4 Models for HGT .............................................................................................. 21 1.5.5 HGT – where do we go from here? ................................................................. 21 1.6 A transcriptomic and phylogenomic approaches to study parasitic plants ................. 22 1.6.1 Driving questions for research on parasitic plants .......................................... 22 1.6.2 Sequencing technologies allow the capture of transcriptomes and genomes ............................................................................................................ 23 1.6.3 The power of phylogenomic approaches (polyploidy (gene duplication) and HGT) .......................................................................................................... 24 1.6.4 Overview of PPGP .......................................................................................... 26 iv Chapter 2 Identification of parasitism genes and the origin of the haustorium ...................... 28 2.1 Introduction to novel traits ......................................................................................... 29 2.2 Results ........................................................................................................................ 31 2.2.1 Assembly statistics and coverage .................................................................... 31 2.2.2 Validation of genes with known roles in Orobanchaceae parasitism .............. 34 2.2.3 Differential gene expression and clustering to identify haustorial genes ........ 36 2.2.4 Shared haustorial genes are enriched for proteolysis and extracellular region localization ............................................................................................ 38 2.2.5 Two examples illustrating haustorial gene expression evolution .................... 42 2.2.6 Identifying haustorial initiation genes and “parasitism genes” ....................... 44 2.2.7 A majority of parasitism genes evolved through gene duplication ................. 47 2.2.8 Regulatory neofunctionalization and origin of the haustorium from root and flower ......................................................................................................... 48 2.2.9 Parasitism genes show signatures of adaptive evolution or relaxed constraint in parasitic lineages ......................................................................... 52 2.2.10 The majority of the parasite-specific sequences have unknown functions ... 54 2.3 Discussion .................................................................................................................
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