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Gene Expression Responses of Larval Gopher (Sebastes Carnatus) and Blue (S

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Gene Expression Responses of Larval Gopher (Sebastes Carnatus) and Blue (S California State University, Monterey Bay Digital Commons @ CSUMB Capstone Projects and Master's Theses Capstone Projects and Master's Theses Fall 2020 Gene Expression Responses of Larval Gopher (Sebastes carnatus) and Blue (S. mystinus) Rockfish ot Ocean Acidification and Hypoxia Jacoby Baker Follow this and additional works at: https://digitalcommons.csumb.edu/caps_thes_all This Master's Thesis (Open Access) is brought to you for free and open access by the Capstone Projects and Master's Theses at Digital Commons @ CSUMB. It has been accepted for inclusion in Capstone Projects and Master's Theses by an authorized administrator of Digital Commons @ CSUMB. For more information, please contact [email protected]. GENE EXPRESSION RESPONSES OF LARVAL GOPHER (SEBASTES CARNATUS) AND BLUE (S. MYSTINUS) ROCKFISH TO OCEAN ACIDIFICATION AND HYPOXIA A Thesis Presented to the Faculty of Moss Landing Marine Laboratories California State University Monterey Bay In Partial Fulfillment of the Requirements for the Degree Master of Science in Marine Science by Jacoby Baker Fall 2020 CALIFORNIA STATE UNIVERSITY MONTEREY BAY The Undersigned Faculty Committee Approves the Thesis of Jacoby Baker: GENE EXPRESSION RESPONSES OF LARVAL GOPHER (SEBASTES CARNATUS) AND BLUE (S. MYSTINUS) ROCKFISH TO OCEAN ACIDIFICATION AND HYPOXIA Scott Hamilton, Chair Moss Landing Marine Laboratories Cheryl Logan, Primary Research Advisor California State Monterey Bay Jonathan Geller Moss Landing Marine Laboratories Nathaniel Jue California State Monterey Bay Daniel Shapiro, Interim Dean Associate VP for Academic Programs and Dean of Undergraduate and Graduate Studies 12/11/2020 Approval Date iii Copyright © 2020 by Jacoby Baker All Rights Reserved iv ABSTRACT Gene Expression Responses of Larval Gopher (Sebastes carnatus) and Blue (S. mystinus) Rockfish to Ocean Acidification and Hypoxia by Jacoby Baker Master of Science in Marine Science California State University Monterey Bay, 2020 Global climate change is driving shifts in ocean chemistry, which combined with intensification of coastal upwelling, reduces ocean pH and dissolved oxygen (DO) content in the nearshore habitats of the California Current System. Physiological plasticity, within and across generations, might be especially important for long-lived, late-to-mature species, like rockfishes (genus Sebastes), that may be unable to keep pace with climate change via genetic adaptation. Rockfishes exhibit matrotrophic viviparity and may be able to buffer their offspring from environmental stress through early developmental exposure or transgenerational plasticity (non-genetic inheritance of phenotypes). In this study, mature female gopher (S. carnatus) and blue (S. mystinus) rockfish were pre-exposed to one of four treatments; 1) control conditions, 2) low pH, 3) low DO, or 4) combined low pH/DO stressors during embryonic growth (i.e. fertilization and gestation), followed by a 5-day larval exposure after birth in either the same or a different treatment received by mothers. I used RNA sequencing to determine how the maternal environment affected larval rockfish gene expression (GE) at birth, after the 5-day larval exposure in either the same maternal treatment or a novel pH/DO environment, and between larvae sampled at birth and after the 5-day larval exposure within each treatment. For both species, I found that the maternal exposure drove larval GE patterns regardless of sampling time point or treatment. Furthermore, the maternal environment continued to strongly influence larval GE for at least the first five days after birth. In gopher rockfish, larvae differentially expressed fewer genes at birth between the control and hypoxic groups than larvae that gestated in and remained in the same treatment and were sampled after the 5-day larval exposure. Gene functions also shifted; at day 5, there was an increase in differentially expressed genes that were related to metabolic pathways, implying that the larvae in the hypoxic treatment are responding to the stressor. In both species, I found that larvae which experienced a pH and/or hypoxic stressor during the maternal exposure had fewer differentially expressed genes across time compared to larvae that experienced control conditions. This pattern remained consistent, even if the larvae were placed into control conditions for the 5-day larval exposure, indicating that exposure to low pH/DO stressors might cause a delay in development. These data suggest that rockfish may not be able to buffer their offspring from environmental stressors, highlighting the important role of the maternal environment during gestation. Between the two species, however, blue rockfish may in fact fare better in future conditions as their reproductive season occurs before the onset of strong spring upwelling, when more hypoxic and low pH water intrudes the nearshore. However, if future climate models are correct, v shifts in the timing and intensity of upwelling season may overlap with the reproductive season in blue rockfish. Elucidating the critical role of the maternal environment on offspring physiology can help us better understand how economically and ecologically important species will fare in the face of climate change. vi TABLE OF CONTENTS PAGE ABSTRACT.............................................................................................................................. iv LIST OF TABLES ................................................................................................................. viii LIST OF FIGURES .................................................................................................................. ix ACKNOWLEDGEMENTS .................................................................................................... xii GENERAL INTRODUCTION .................................................................................................. 1 CHAPTER 1 GOPHER ROCKFISH ................................................................................................... 5 Introduction .............................................................................................................. 5 Methods ................................................................................................................... 9 Experimental Setup ................................................................................................ 10 Larvae Collection ................................................................................................... 11 Total RNA Extraction ............................................................................................ 11 mRNA Isolation and cDNA Synthesis .................................................................. 12 Read Processing, de novo Assembly, and Annotation ........................................... 12 Differential Gene Expression Quantification ......................................................... 13 Results .................................................................................................................... 15 Fish Husbandry and Larval Collections ................................................................. 15 RNA Sequencing and De Novo Transcriptome Assembly .................................... 16 Effects of Maternal Environment on Larval Gene Expression Patterns ................ 16 Maternal Influence Amplified Over Time ............................................................. 18 Discussion .............................................................................................................. 19 Maternal Influence on Larval Gene Expression Patterns ....................................... 20 Maternal Influences Amplified Over Time ............................................................ 22 Gestational Exposure to Hypoxia Reduces Gene Expression Variability in Larvae .................................................................................................................... 24 Limitations in the Project ....................................................................................... 25 How Gopher Rockfish Will Fare Under Future Hypoxic Conditions.................... 26 2 BLUE ROCKFISH ...................................................................................................... 28 Introduction ............................................................................................................ 28 Methods ................................................................................................................. 34 Experimental Setup ................................................................................................ 34 vii Larval Collection ................................................................................................... 35 Total RNA Extraction ............................................................................................ 35 mRNA Isolation and cDNA Synthesis .................................................................. 36 Read Processing, de novo Assembly, and Annotation .......................................... 37 Differential Gene Expression Quantification ........................................................ 37 Visualization of Gene Expression Data ................................................................. 39 Results .................................................................................................................... 40 Fish Husbandry and Larval Collections ................................................................
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