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Comparative Evolutionary Analysis of Organellar Genomic Diversity in Green Plants Weishu Fan University of Nebraska - Lincoln

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Comparative Evolutionary Analysis of Organellar Genomic Diversity in Green Plants Weishu Fan University of Nebraska - Lincoln University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Theses, Dissertations, and Student Research in Agronomy and Horticulture Department Agronomy and Horticulture Summer 7-26-2016 Comparative Evolutionary Analysis of Organellar Genomic Diversity in Green Plants Weishu Fan University of Nebraska - Lincoln Follow this and additional works at: http://digitalcommons.unl.edu/agronhortdiss Part of the Agronomy and Crop Sciences Commons, Genetics and Genomics Commons, and the Plant Breeding and Genetics Commons Fan, Weishu, "Comparative Evolutionary Analysis of Organellar Genomic Diversity in Green Plants" (2016). Theses, Dissertations, and Student Research in Agronomy and Horticulture. 110. http://digitalcommons.unl.edu/agronhortdiss/110 This Article is brought to you for free and open access by the Agronomy and Horticulture Department at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Theses, Dissertations, and Student Research in Agronomy and Horticulture by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. COMPARATIVE EVOLUTIONARY ANALYSIS OF ORGANELLAR GENOMIC DIVERSITY IN GREEN PLANTS by Weishu Fan A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy Major: Agronomy and Horticulture Under the Supervision of Professor Jeffrey P. Mower Lincoln, Nebraska July, 2016 COMPARATIVE EVOLUTIONARY ANALYSIS OF ORGANELLAR GENOMIC DIVERSITY IN GREEN PLANTS Weishu Fan, Ph.D. University of Nebraska, 2016 Advisor: Jeffrey P. Mower The mitochondrial genome (mitogenome) and plastid genome (plastome) of plants vary immensely in genome size and gene content. They have also developed several eccentric features, such as the preference for horizontal gene transfer of mitochondrial genes, the reduction of the plastome in non-photosynthetic plants, and variable amounts of RNA editing affecting both genomes. Different organismal lifestyles can partially account for the highly diverse organellar genomes across the tree of green plants. For example, endosymbiotic and parasitic lifestyles can dramatically affect the genomic architectures of plant mitochondria and plastids. In this study, the organellar genomes of several green plants with atypical lifestyles were investigated and compared with the breadth of organelle genomic diversity within green plants. Next-generation sequencing and comparative evolutionary analyses were performed on organellar genomes of parasitic plants in Orobanchaceae and endosymbiotic algae in Chlorellaceae. Comparative organellar genomic analysis from endosymbiotic green algae provided no evidence for genome reduction; instead the endosymbiont genomes are generally larger in genome size and richer in intron content. Similarly, facultative hemiparasitic species in Orobanchaceae revealed minimal organellar genome degradation, but some evidence for several horizontal transferred genes. In both groups, the lack of genomic reduction may be attributed to the retention of photosynthetic ability. In addition, the extent of RNA editing was examined in the mitogenome of Welwitschia, a xerophytic plant. RNA editing sites in Welwitschia are extremely reduced compared with other gymnosperms, and may be caused by retroprocessing. Taken together, these results demonstrated that atypical lifestyle does not necessarily lead to the production of unusual genomic features and exhibited the convergence and divergence in green plants organelle genomes. III ACKNOWLEDGEMENTS First and foremost, I would like to express my special appreciation and thanks to my advisor Dr. Jeffrey P. Mower. He has been a tremendous mentor for me. I appreciate all his contributions of ideas and time to make my Ph.D. program stimulating and effective. His enthusiasm and continuous innovation on the research was contagious and motivational for me, especially during tough times in the journey. He has provided an excellent example for being a scientist and professor. My gratitude to him is magnified by his warm personality and constant encouragement and support. Secondly, I would like to recognize my committee members: Dr. Heriberto Cerutti, Dr. Thomas E. Elthon and Dr. Wayne Riekhof for serving as my committee members, and for their time, interest, brilliant comments and insightful suggestions. I am thankful to Dr. Sally Mackenzie’s lab, Dr. Kenneth Nickerson’s lab, Dr. Wayne Riekhof’s lab and Dr. Steve Harris’ lab for their generous sharing of facilities and chemicals with us. I also sincerely thank my previous advisor Dr. Gaihe Yang for his support and encouragement. My colleagues in the Mower Lab have contributed immensely to my professional and personal time at Lincoln. I am especially grateful to Dr. Wenhu Guo for his constant help, collaborations and constructive advice in my research and career. I also appreciate the comments and suggestions from Dr. Andan Zhu. I would like to acknowledge former and present lab members: Nancy Hepburn, Dr. Kanika Jain, Dr. Brandi Sigmon, Dr. Felix Grewe, Lexis Funk and Yan Li for their invaluable input to my dissertation and friendship. IV I also acknowledge the funding source that made my Ph.D. work in U.S. possible. I was funded by a fellowship from the China Scholarship Council for four successive years. My work was also supported by the National Science Foundation and Center for Plant Science Innovation. My time at University of Nebraska-Lincoln was made enjoyable in large part due to the many friends that became a part of my life. I cannot thank enough Jyothi Kumar, Sunil Kumar, Ruvini Pathirana, Jithesh, Amit, Yuan, Wenjin, Ting, Xin, Wenjia, Fei, Guangchao, Qian and many other friends for being so nice and bringing memorable times. Lastly, I would like to thank my families, especially my mom Xiuzhi Li, my sister Chao Fan and my best friend Peng Wang, for all their unconditional love and encouragement, for their faithful support and patience. Thank you. V TABLE OF CONTENTS LIST OF TABLES ........................................................................................................ VII LIST OF FIGURES ..................................................................................................... VIII CHAPTER 1: Literature Review .................................................................................... 1 1 Introduction ................................................................................................................. 2 2 Green Plants Organelle Genome Sequencing Progress ............................................... 3 3 Plant Organellar Genome Size and Genetic Content Diversity ................................... 5 3.1 Plant Mitochondrial Genome ............................................................................... 5 3.1.1 Genome Size ................................................................................................. 5 3.1.2 Gene Content ................................................................................................. 6 3.1.3 Intron Content ............................................................................................... 7 3.2 Plant Plastid Genome ........................................................................................... 8 3.2.1 Genome Structure and Genome Size Diversity ............................................ 8 3.2.2 Gene Content ................................................................................................. 9 3.2.3 Intron Content ............................................................................................. 10 4 Peculiar Features of Plant Organellar Genomes ........................................................ 10 4.1 Horizontal Gene Transfer in Plant Mitochondrial Genome ............................... 11 4.2 RNA Editing in Plant Mitochondrial Genome................................................... 12 4.2.1 Variation in the Frequency of RNA Editing ............................................... 13 4.2.2 RNA Rditing Loss with Retroprocessing .................................................... 14 4.3 Plastid Genome Reduction in Parasitic Plants ................................................... 15 5 Research Goals .......................................................................................................... 16 REFERENCES ............................................................................................................. 19 TABLES ....................................................................................................................... 30 CHAPTER 2: Comparative Organellar Genomics of Chlorellales: Genomic Effects of an Endosymbiont Lifestyle? ...................................................................................... 32 ABSTRACT .................................................................................................................. 33 INTRODUCTION ........................................................................................................ 34 MATERIALS AND METHODS .................................................................................. 37 RESULTS ..................................................................................................................... 41 DISCUSSION ............................................................................................................... 47 ACKNOWLEDGMENTS ...........................................................................................
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