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Foamy-Like Endogenous Retroviruses Are Abundant and Extensive in Teleosts

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Foamy-Like Endogenous Retroviruses Are Abundant and Extensive in Teleosts Foamy-like Endogenous Retroviruses Are Abundant and Extensive In Teleosts Item Type text; Electronic Thesis Authors Ruboyianes, Ryan Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 05/10/2021 23:26:24 Link to Item http://hdl.handle.net/10150/594955 FOAMY-LIKE ENDOGENOUS RETROVIRUSES ARE ABUNDANT AND EXTENSIVE IN TELEOSTS by RYAN RUBOYIANES ____________________________ Copyright © Ryan Ruboyianes 2015 A Thesis Submitted to the Faculty of the DEPARTMENT OF ECOLOGY & EVOLUTIONARY BIOLOGY In Partial Fulfillment of the Requirements For the Degree of MASTER OF SCIENCE In the Graduate College THE UNIVERSITY OF ARIZONA 2015 STATEMENT BY AUTHOR The thesis titled Foamy-like Endogenous Retroviruses Are Abundant and Extensive in Teleosts prepared by Ryan Ruboyianes has been submitted in partial fulfillment of requirements for a master’s degree at the University of Arizona and is deposited in the University Library to be made available to borrowers under rules of the Library. Brief quotations from this thesis are allowable without special permission, provided that an accurate acknowledgement of the source is made. Requests for permission for extended quotation from or reproduction of this manuscript in whole or in part may be granted by the copyright holder. SIGNED: Ryan Ruboyianes APPROVAL BY THESIS DIRECTOR This thesis has been approved on the date shown below: _______________________ Dr. Michael Worobey Date Professor of Ecology & Evolutionary Biology 2 ACKNOWLEDGEMENTS I would like to thank, from the depths of my heart, Tom Watts, for his technical and moral guidance towards completing this stage of my education. I thank my research advisor, Dr. Michael Worobey, and thesis committee members, Dr. Michael Barker and Dr. John Wiens, for patience and timely advice. Dr. Worobey, thank you especially for the necessary and sometimes difficult lessons in self-sufficiency. I again thank Dr. Barker, and Dr. Mark Beilstein, for the friendly encouragement that came with their good advice. I thank Dr. Guan-Zhu Han and Brendan Larsen, my lab-mates and comrades, for immensely helpful suggestions for improving my work. I thank Kelsey Yule and Sarah Richman for the many helpful discussions. I thank my father for reminding me that I am not stupid. I gratefully thank all of the people who graciously provided samples for my experiments; Andrew Bentley, Dr. Kevin Fitzsimmons and Dawn M. Cloutier Wyles were especially helpful. Mom, thank you for literally everything else. TABLE OF CONTENTS LIST OF FIGURES .........................................................................................................................5 LIST OF TABLES ...........................................................................................................................5 ABSTRACT .....................................................................................................................................6 INTRODUCTION ...........................................................................................................................7 RESULTS AND DISCUSSION ......................................................................................................9 Foamy-like ERVs in Fish Genomes ........................................................................................................9 Foamy Virus Sister Clade Comprised of Fish ERVs ..........................................................................13 Fish Foamy-like ERVs More Complex Than FVs ..............................................................................15 Genetic organization .........................................................................................................................15 Fish ERV foamy-like features ..........................................................................................................20 Estimated Age of ERV Integration ......................................................................................................23 Virus-Host Cophylogenetic History .....................................................................................................27 De Novo Sequencing of FV-like Sequences in Diverse Teleosts .........................................................29 MATERIALS AND METHODS ...................................................................................................33 Genome screening ..............................................................................................................................33 De novo fish ERV sequencing ...........................................................................................................33 Phylogenetic analysis .........................................................................................................................35 Quasi-consensus construction and annotation ...............................................................................36 ERV age estimation ...........................................................................................................................36 CONCLUSIONS ...........................................................................................................................37 REFERENCES ..............................................................................................................................40 APPENDIX A – RETROVIRUS SEQUENCES IN PHYLOGENETIC ANALYSES ................47 APPENDIX B – SAMPLED FISH SPECIES ...............................................................................50 4 LIST OF FIGURES Figure 1. Retrovirus Pol phylogeny. Representative taxa from all classified genera of exogenous and endogenous retrovirus are included with all known fish foamy-like endogenous retroviruses in a Bayesian phylogenetic tree construct. .................................................................14 Figure 2. Fish ERV genetic features. Detailed genetic features of prototype foamy virus and three high-quality fish ERVs. Foamy-like ERV features are annotated. .......................................16 Figure 3. Fish ERV genetic organization. Coarse to-scale comparison of intact fish ERVs with annotated genes. .............................................................................................................................19 Figure 4. Foamy clade host-virus incongruence. A cophylogeny and tanglegram designed to test apparent incongruences between foamy-like fish ERV host and virus phylogenies. Host and virus trees are compared for only highly intact fish ERVs. Crossed lines show that even recently integrated ERVs demonstrate a history of host switching. ............................................................28 Figure 5. Phylogeny of 27 foamy-like fish ERVs and distant RVs. Bayesian reconstruction of phylogenetic history for all fish EFVs recovered in this study, including the those previously described. .......................................................................................................................................32 LIST OF TABLES Table 1. EFV-harboring fish genome contigs. Included are the WGS contig from each actinopterygian host with the highest sequence homology to exogenous foamy viruses. .............10 Table 2. Estimates of ERV integration age. Time since integration for fish ERVs with intact LTR. Ages calculated with LTR divergence and LTR-flank divergence method. ........................25 Table 3. Hosts with EFV-like fragments from de novo sequencing. Detected by PCR assay of hosts with no GenBank genome representation. Included are novel EFV fragments with homology to exogenous foamy viruses. .........................................................................................30 5 ABSTRACT Spumaretrovirus, among retrovirus clades, has an extensive accumulation of evidence for an ancient origin. Recent discoveries indicate that the Spumaretrovirus ancestor could have been the first retrovirus to appear during the evolution of vertebrates. If they indeed appeared in ancient marine environments hundreds of millions of years ago, we should expect significant undiscovered diversity of foamy-like endogenous retroviruses in fish genomes. I report the discovery of these elements in 23 novel teleost hosts. These viruses have very large genomes compared to all other retroviruses, possess an unprecedented array of accessory genes, and form a robust reciprocally monophyletic sister clade with sarcopterygian host foamy viruses, with class III mammal endogenous retroviruses being the immediate sister group to both clades. I estimated that some of these viruses integrated recently into host genomes, and exogenous descendants of these viruses may be extant. 6 INTRODUCTION Foamy viruses (FV) constitute one of seven extant genera of Retroviridae (1). The lone genus of the Spumaretrovirinae subfamily, FVs are complex retroviruses distinguished from Orthoretrovirinae primarily because of disparate replication strategies (2). FV infection is persistent and nonpathogenic in vivo, but causes characteristic fluid-filled syncytial vacuoles in vitro with a “foamy” appearance (3,4). Known infectious FVs are thus far confined to mammalian hosts (5), including felines (6), horses (7), cows (8), bats (9), and wide variety of primates
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