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Transcriptomics Analysis Gene Expression and Effects of Acute Exposure to Experimental Temperatures and Salinities on the Surviv

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Transcriptomics Analysis Gene Expression and Effects of Acute Exposure to Experimental Temperatures and Salinities on the Surviv TRANSCRIPTOMICS ANALYSIS GENE EXPRESSION AND EFFECTS OF ACUTE EXPOSURE TO EXPERIMENTAL TEMPERATURES AND SALINITIES ON THE SURVIVAL OF SOUTHERN FLOUNDER (Paralichthys lethostigma) PREMETAMORPHIC LARVAE SPAWNED BY PARENTS COLLECTED ALONG THE ENVIRONMENTAL CLINE OF THE TEXAS COAST A Dissertation by Ivonne Rodriguez Blandon Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Frances I. Gelwick Co-Chair of Committee, Jing Cai Committee Members, Robert R. Vega Delbert M. Gatlin III Head of Department, David Caldwell December 2018 Major Subject: Wildlife and Fisheries Sciences Copyright 2018 Ivonne R. Blandon ABSTRACT Southern flounder (Paralichthys lethostigma) provides important commercial and recreational fisheries opportunities on the Texas coast. The economic impact of this fishery is negatively affected by recent declines in harvest throughout the geographic range of this species. Environmental variables that may be important determinants of Southern flounder abundance and fishery productivity include freshwater inflows, extent and type of the nursery habitat and changes in temperature regimes related to climate change. Despite progressive harvest regulations to manage the population decline and protect the adult spawning migration to the Gulf of Mexico, the Southern flounder population has not recovered to its historical level. The Texas Parks and Wildlife Department is implementing a stock enhancement program for Southern flounder to supplement natural populations on the Texas bays. A critical phase of the program is to validate at large scale the larval and juvenile production protocols available for Southern flounder to optimize physical environmental parameters that influence survival during larval rearing. Temperature and salinity are two ubiquitous abiotic factors that influence all biological functions of these two early life history stages and survival. I exposed Southern flounder eggs and premetamorphic larvae to different temperature and salinities found on the environmental cline of the Texas coast to evaluate the effect of these conditions on survival of individuals spawned by broodstock collected from different environments of coastal Texas. RNA next generation sequencing was used to generate more than 29,000 sequences that were assembled in a de novo transcriptome. Temperature was the most important factor affecting the survival of Southern flounder at these two stages of development. Synergy between temperature, salinity, and site of collection of the parents also played a role in fish survival in response to the temperature and salinity challenges. ii From the sequences, 96% were mapped and used to identify proteins, genes and biological gene functions. The number of up-regulated genes and gene expression was higher for temperatures and salinity in Sabine and Aransas fish than in Galveston. iii DEDICATION I dedicate this work to the great people of the State of Texas and their natural resources. During an important segment of my professional life Texas’s natural resources have been a source of inspiration and motivation for my work. iv ACKNOWLEDGEMENTS I feel indebted to my graduate committee professors Dr. Frances Gelwick, Dr. James Cai, Dr. Delbert Gatlin and Dr. Robert R. Vega for their mentoring, guidance, and patience. I thank the Texas Parks and Wildlife Department and the Coastal Fisheries Division for their support. I am beholden to my supervisor Dr. Robert R. Vega, for his words of wisdom, discipline and leadership to guide me during graduate school, he mediated to find the resources and work schedule flexibility to complete the research. During the course of the research, I received the help of many of my colleagues in the hatchery program, I am grateful to Jennifer Buttler, Jeff Bayer, Courtney Moore, Paul Cason, David Abrego, and the technical personnel at Sea Center of Texas for providing the fish from Galveston Bay and Sabine Lake for the studies. My heart is full of appreciation to my colleague Ruben Chavez and the technical personnel at the Marine Development Center for their assistance. Thank you to Robert Adami for the edits of the initial proposal and to Whitney Mackline for her assistance. My sincere gratitude to the Saltwater Enhancement Association in Corpus Christi for providing the funds to collect the fish from Aransas Bay and to my colleagues at the University of Texas Marine Science Institute, Jeff Kaiser and Cindy Faulk for providing valuable advice and biological materials for the studies. Dr. Divhya Arassapan, Dr. Ence Yang and Benny Goetz of the University of Texas at Austin are also acknowledged for their assistance with the transcriptome assemblage. The assistance of Dr. James Cai and Dr. Frances Gelwick on experimental design and statistical analysis was invaluable. I am humble with this experience and my love and thanksgiving goes to God. Max thank you for walking at my side on this trail with such patience and love. My sons Carlos Jose and v Omar Jose and my family always have been the foundation of my innermost strength. I feel blessed with their love and prayers. vi CONTRIBUTORS AND FUNDING SOURCES Contributors This work was supervised by a dissertation committee consisting of Dr. Frances Gelwick and Dr. Delbert Gatlin (Wildlife Fisheries Sciences), Dr. James Cai (Veterinary Medicine and Biomedical Sciences) and Dr. Robert R. Vega (Texas Parks and Wildlife Department Coastal Fisheries). Dr. Divhya Arassapan, Dr. Ence Yang and Benny Goetz (University of Texas at Austin) assisted with the transcriptome assemblage. All other work conducted for the dissertation was completed by the student independently. Funding Sources This project was funded by the Federal Aid and Sport Fish Restoration to Texas Parks and Wildlife Department. vii TABLE OF CONTENTS Page ABSTRACT ....................................................................................................................... ii DEDICATION .................................................................................................................. iv ACKNOWLEDGEMENTS ............................................................................................... v CONTRIBUTORS AND FUNDING SOURCES ........................................................... vii TABLE OF CONTENTS ................................................................................................ viii LIST OF FIGURES ........................................................................................................... x LIST OF TABLES .......................................................................................................... xiii CHAPTER I INTRODUCTION AND LITERATURE REVIEW .................................... 1 CHAPTER II EFFECTS ON DEVELOPMENT AND SURVIVAL OF NEWLY-HATCHED LARVAE OF SOUTHERN FLOUNDER (PARALICHTHYS LETHOSTIGMA) FROM ARANSAS, TEXAS UNDER CONDITIONS OF ACUTE EXPOSURE TO EXPERIMENTAL TEMPERATURE AND SALINITY TREATMENT COMBINATIONS.8 Introduction ........................................................................................................ 8 Materials and Methods ..................................................................................... 12 Results .............................................................................................................. 15 Discussion ........................................................................................................ 23 CHAPTER III EFFECTS OF EXPOSURE TO TEMPERATURE AND SALINITY COMBINATIONS ON THE SURVIVAL OF SOUTHERN FLOUNDER (PARALICHTHYS LETHOSTIGMA) PREMETAMORPHIC LARVAE SPAWNED BY PARENTS COLLECTED ALONG THE ENVIRONMENTAL CLINE OF THE TEXAS COAST. 26 Introduction ...................................................................................................... 26 Materials and Methods ..................................................................................... 28 Results .............................................................................................................. 33 Discussion ........................................................................................................ 42 CHAPTER IV TRANSCRIPTOMIC ANALYSIS OF PHYSIOLOGICAL RESPONSES OF SOUTHERN FLOUNDER (PARALICHTHYS LETHOSTIGMA) PREMETAMORPHIC LARVAE EXPOSED TO HIGH TEMPERATURE AND SALINITY .......................... 48 Introduction ...................................................................................................... 48 Materials and Methods ..................................................................................... 52 viii Results .............................................................................................................. 62 Discussion ........................................................................................................ 84 CHAPTER V CONCLUSIONS ...................................................................................... 92 REFERENCES ................................................................................................................ 94 APPENDIX A SOUTHERN FLOUNDER REARING PROTOCOL .......................... 121 ix LIST OF FIGURES PAGE Fig. 1. Plot of the effect of temperature (°C) on larval survival. Points show proportion of larvae surviving at each temperature treatment. The line represents the generalized linear model with binomial error distribution. Darker shaded area represents one standard deviation of
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