University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2016 Comparative Genomics of Ape Plasmodium Parasites Reveals Key Evolutionary Events Leading to Human Malaria Sesh Alexander Sundararaman University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Evolution Commons, Genetics Commons, and the Microbiology Commons Recommended Citation Sundararaman, Sesh Alexander, "Comparative Genomics of Ape Plasmodium Parasites Reveals Key Evolutionary Events Leading to Human Malaria" (2016). Publicly Accessible Penn Dissertations. 2046. https://repository.upenn.edu/edissertations/2046 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/2046 For more information, please contact [email protected]. Comparative Genomics of Ape Plasmodium Parasites Reveals Key Evolutionary Events Leading to Human Malaria Abstract African great apes are infected with at least six species of P. falciparum-like parasites, including the ancestor of P. falciparum. Comparative studies of these parasites and P. falciparum (collectively termed the Laverania subgenus) will provide insight into the evolutionary origins of P. falciparum and identify genetic features that influence host tropism. Here we show that ape Laverania parasites do not serve as a recurrent source of human malaria and use novel enrichment techniques to derive near full-length genomes of close and distant relatives of P. falciparum. Using a combination of single template amplification and deep sequencing, we observe no evidence of ape Laverania infections in forest dwelling humans in Cameroon. This result supports previous findings that ape Laverania parasites are host specific and have successfully colonized humans only once. To understand the determinants of host specificity and identify genetic characteristics unique to P. falciparum, we develop a novel method for selective enrichment of Plasmodium DNA from sub-microscopically infected whole blood samples. We use this technique to enrich for Laverania genomic DNA from chimpanzee blood samples and assemble near full length genomes for both close (P. reichenowi) and distant (P. gaboni) relatives of P. falciparum. Comparative analyses of these genomes to P. falciparum identify features that are conserved across the Laverania subgenus, including the expansion of the FIKK kinases and the presence of var-like multigene families in all Laverania species. Our analyses also identify genetic features that are unique to P. falciparum, such as a very low within-species diversity and a complex evolutionary history of the essential invasion genes RH5 and CyRPA. This dissertation lays the groundwork for future comparative analyses of the Laverania subgenus including population genomic analyses of ape parasites and comparisons of P. falciparum to its ancestor, P. praefalciparum. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Beatrice H. Hahn Second Advisor Frederic D. Bushman Keywords Evolution, Great Ape, Malaria, Plasmodium, Zoonosis Subject Categories Evolution | Genetics | Microbiology This dissertation is available at ScholarlyCommons: https://repository.upenn.edu/edissertations/2046 COMPARATIVE GENOMICS OF APE PLASMODIUM PARASITES REVEALS KEY EVOLUTIONARY EVENTS LEADING TO HUMAN MALARIA Sesh A. Sundararaman A DISSERTATION in Cell and Molecular Biology Presented to the Faculties of the University of Pennsylvania in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy 2016 Supervisor of Dissertation Co-Supervisor of Dissertation ______________________ _________________________ Beatrice H. Hahn Frederic D. Bushman Professor of Medicine Professor of Microbiology Graduate Group Chairperson _________________________ Daniel S. Kessler Associate Professor of Cell and Developmental Biology Dissertation Committee Robert W. Doms, Chair and Pathologist in Chief, Children’s Hospital of Philadelphia Dustin Brisson, Associate Professor of Biology David S. Roos, E. Otis Kendall Professor of Biology Sarah A. Tishkoff, David and Lyn Silfen University Professor COMPARATIVE GENOMICS OF APE PLASMODIUM PARASITES REVEALS KEY EVOLUTIONARY EVENTS LEADING TO HUMAN MALARIA © COPYRIGHT 2015 Sesh A. Sundararaman This work is licensed under the Creative Commons Attribution- NonCommercial-ShareAlike 3.0 License To view a copy of this license, visit http://creativecommons.org/licenses/by-ny-sa/2.0/ DEDICATION Dedicated to the memories of Wiley A. Green and Raghavachari Desikan iii ACKNOWLEDGMENT I would like to thank Beatrice Hahn and Rick Bushman for their support and guidance over the last five years. They gave me the freedom to explore and learn while keeping me focused and refining my scientific thinking. I thank my undergraduate advisors Claire Ting and Manuel Llinàs starting me on this journey. I also thank my committee members, Bob Doms, David Roos, Sarah Tishkoff, and Dustin Brisson for their support of both my research and my development as a scientist. This work could not have been completed without the help of many others in both the Hahn and Bushman labs and beyond. Kyle Bittinger, Nirav Malani, Scott Sherrill-Mix, and Aubrey Bailey taught me the fundamentals of coding in R, perl and python. Weimin Liu, Yingying Li, Gerald Learn, Shilpa Iyer, Fred Bibollet-Ruche, introduced me to the techniques that they have refined in their time in the Hahn lab. I was lucky to have so many collaborators including Dorothy Loy, Ahidjo Ayouba, Jordan Malenke, Katharina Shaw, Erik Clarke, Stephanie Seifert, Dan Larremore, and Will Proto. Lindsey Plenderleith and Paul Sharp were a constant source of guidance. Lindsey was also a driving force in the assembly and analysis of the ape Laverania genomes. I also thank the Bushman, Hahn, Shaw, and Bar labs, especially Ben Scheinfeld, Tuhina Srivastava, Frances Male, Ranjit Warrier, Ronnie Russell, Eunlim Kim, Hannah Barbian, Marcus Gondim, Nick Parrish, Erica Parrish, Patricia Crystal, Shivani Sethi, Arwa Abbas, Brendan Kelly, Casey Hofstaeder, Young Hwang, Andrew Smith, Ted Kreider, Abby Lauder, Alice Laughlin, Alexandra Bryson, and Anatoly Dryga. I especially thank my family and friends for their constant support throughout my life. Without the interest in science and learning instilled in me by my parents, I would not have achieved half of what I have today. Finally, Charlie, my constant canine companion. He is the best dog that I could ever wish for. iv ABSTRACT COMPARATIVE GENOMICS OF APE PLASMODIUM PARASITES REVEALS KEY EVOLUTIONARY EVENTS LEADING TO HUMAN MALARIA African great apes are infected with at least six species of P. falciparum-like parasites, including the direct ancestor of P. falciparum. Comparative studies of these parasites and P. falciparum (collectively termed the Laverania subgenus) will provide insight into the evolutionary origins of P. falciparum and identify genetic features that influence host tropism. Here we show that ape Laverania parasites do not sperve as a recurrent source of human malaria and use novel enrichment techniques to derive near full-length genomes of close and distant relatives of P. falciparum. Using a combination of single template amplification and deep sequencing, we observe no evidence of ape Laverania infections in forest dwelling humans in Cameroon. This result supports previous findings that ape Laverania parasites are host specific and have successfully colonized humans only once. To understand the determinants of host specificity and identify genetic characteristics unique to P. falciparum, we develop a novel method for selective enrichment of Plasmodium DNA from sub-microscopically infected whole blood samples. We use this technique to enrich for Laverania genomic DNA from chimpanzee blood samples and assemble near full length genomes for both close (P. reichenowi) and distant (P. gaboni) relatives of P. falciparum. Comparative analyses of these genomes to P. falciparum identify features that are conserved across the Laverania subgenus, including the expansion of the FIKK kinases and the presence of var-like multigene families in all Laverania species. Our analyses also identify genetic features that are unique to P. falciparum, such as a very low within-species diversity and a complex v evolutionary history of the essential invasion genes RH5 and CyRPA. This dissertation lays the groundwork for future comparative analyses of the Laverania subgenus including population genomic analyses of ape parasites and comparisons of P. falciparum to its ancestor, P. praefalciparum. vi TABLE OF CONTENTS ABSTRACT ...................................................................................................................... V LIST OF TABLES ............................................................................................................ IX LIST OF ILLUSTRATIONS .............................................................................................. X CHAPTER 1 – MALARIA PARASITES OF THE GREAT APES ..................................... 1 1.1 The Epidemiology and Biology of Malaria ............................................................. 1 1.2 Plasmodium Species in African Great Apes .......................................................... 2 1.3 The Origin of Human Malaria ................................................................................... 4 1.4 Elucidating the Steps to the Emergence of P. falciparum ...................................