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Molecular Evolutionary Analysis of Plastid Genomes in Nonphotosynthetic Angiosperms and Cancer Cell Lines

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Molecular Evolutionary Analysis of Plastid Genomes in Nonphotosynthetic Angiosperms and Cancer Cell Lines The Pennsylvania State University The Graduate School Department or Biology MOLECULAR EVOLUTIONARY ANALYSIS OF PLASTID GENOMES IN NONPHOTOSYNTHETIC ANGIOSPERMS AND CANCER CELL LINES A Dissertation in Biology by Yan Zhang 2012 Yan Zhang Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Dec 2012 The Dissertation of Yan Zhang was reviewed and approved* by the following: Schaeffer, Stephen W. Professor of Biology Chair of Committee Ma, Hong Professor of Biology Altman, Naomi Professor of Statistics dePamphilis, Claude W Professor of Biology Dissertation Adviser Douglas Cavener Professor of Biology Head of Department of Biology *Signatures are on file in the Graduate School iii ABSTRACT This thesis explores the application of evolutionary theory and methods in understanding the plastid genome of nonphotosynthetic parasitic plants and role of mutations in tumor proliferations. We explore plastid genome evolution in parasitic angiosperms lineages that have given up the primary function of plastid genome – photosynthesis. Genome structure, gene contents, and evolutionary dynamics were analyzed and compared in both independent and related parasitic plant lineages. Our studies revealed striking similarities in changes of gene content and evolutionary dynamics with the loss of photosynthetic ability in independent nonphotosynthetic plant lineages. Evolutionary analysis suggests accelerated evolution in the plastid genome of the nonphotosynthetic plants. This thesis also explores the application of phylogenetic and evolutionary analysis in cancer biology. Although cancer has often been likened to Darwinian process, very little application of molecular evolutionary analysis has been seen in cancer biology research. In our study, phylogenetic approaches were used to explore the relationship of several hundred established cancer cell lines based on multiple sequence alignments constructed with variant codons and residues across 494 and 523 genes. Phylogenetic analysis revealed that phylogenetic clustering of cancer cell lines might reflect the functional similarities in cellular pathways. Molecular evolutionary analysis was applied to identify potential driver mutations that are causally implicated in oncogenesis. Our study indicates phylogenetic and molecular evolutionary analysis can provide important insights tumor classification and the development of novel anticancer strategies, and suggests the potential role of evolutionary history and methods in cancer diagnostics and therapeutics. iv TABLE OF CONTENTS LIST OF FIGURES ................................................................................................................. vi LIST OF TABLES ................................................................................................................... viii ACKNOWLEDGEMENTS ..................................................................................................... ix Chapter 1 Introduction ........................................................................................................... 1 References ........................................................................................................................ 9 Chapter 2 Striking parallelism of plastid genome structure and dynamics in independent nonphotosynthetic lineages (this is a Heading 1 style) .................................................... 11 Abstract ........................................................................................................................... 12 Introduction ...................................................................................................................... 14 Materials and Methods .................................................................................................... 19 Plastome sequencing ................................................................................................ 19 Indel analysis in inverted repeats and pseudogenes ................................................ 21 Phylogenetic anlaysis .............................................................................................. 22 Molecular evolutionary analysis ............................................................................. 23 Results ............................................................................................................................. 25 Plastid genome size and structure ............................................................................ 25 Gene content ........................................................................................................... 32 Analysis of indels .................................................................................................... 38 Genes for gene expression ...................................................................................... 42 Pholisma and Epifagus are independently derived ................................................. 42 Molecular evolutionary analyses ............................................................................ 43 Relaxed clock analysis ............................................................................................ 50 Discussion ....................................................................................................................... 53 Plastome phylogeny ................................................................................................. 53 Plastome structure and evolutionary dynamics ....................................................... 54 Holoparasitism occurred more recently in Pholisma than in Epifagus .................... 61 Parallel polymorphoism of rbcL in independent holoparasitic lineages ................. 62 Deterministic and stochastic evolution model of plastomes in parasitic plants ..... 64 Is this a convergence or parallelism? ...................................................................... 65 References ....................................................................................................................... 67 Chapter 3 Plastid genome sequence and analysis of Conopholis americana, a holoparasitic relative of Epifagus virginiana ................................................................... 72 Abstract ........................................................................................................................... 72 Introduction ..................................................................................................................... 73 Materials and Methods .................................................................................................... 76 DNA extraction and fosmid library ......................................................................... 76 Procedure for fosmid shotgun sequencing and sequence assembly ........................ 77 v Genome annotation ................................................................................................. 78 Molecular evolutionary anlaysis ............................................................................. 78 Results ............................................................................................................................. 78 Discussion ....................................................................................................................... 90 References ........................................................................................................................ 95 Chapter 4 Molecular Evolutionary Analysis of Cancer Cell Lines .......................................... 101 Abstract ...................................................................................................................... 102 Introduction ..................................................................................................................... 103 Materials and Methods ..................................................................................................... 106 DNA sequencing .................................................................................................... 106 Construction of multiple sequence alignments ...................................................... 107 Phylogenetic analysis ............................................................................................ 109 mRNA expression and pathway analysis ............................................................... 110 Selection pressure analysis .................................................................................... 111 Results and Discussion .................................................................................................... 111 References ....................................................................................................................... 128 Chapter 5 Future Work ........................................................................................................... 132 References ............................................................................................................................... 135 Appendix A Flowchart of molecular evolutionary analysis in chapter 2 ................................ 136 Appendix B Gene summary by function category in Pholisma, Epifagus, Ehretia and Mimulus ............................................................................................................................ 137 Appendix C Comparative plastome summary of Pholisma, Epifagus, Ehretia and Mimulus ...........................................................................................................................
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