The Two Genomes of Gilthead Sea Bream (Sparus aurata): a Multi-Omics and Holobiont Approach

Abstract

Summaries and Glossary 1. General Introduction 1.1. Aquaculture 1.2. Omics 2. Aims, outline, and institutional support 2.1. Aims 2.2. Outline 2.3. Institutional support 3. Transcriptomic profiling of Gh/Igf system reveals a prompted tissuespecific differentiation and novel hypoxia responsive genes in gilthead sea bream Abstract 3.1. Introduction 3.2. Results 3.3. Discussion 3.4. Methods Supplementary Material 4. Targeting the Mild-Hypoxia Driving Force for Metabolic and Muscle Transcriptional Reprogramming of Gilthead Sea Bream (Sparus aurata) Juveniles Simple summary Abstract 4.1. Introduction 4.2. Material and Methods 4.3. Results 4.4. Discussion 4.5. Conclusions Supplementary material 5. Broodstock nutritional programming differentially affects the hepatic transcriptome and genome-wide DNA methylome of farmed gilthead sea bream (Sparus aurata) depending on genetic background Abstract 5.1. Background 5.2. Results 5.3. Discussion 5.4. Conclusions 5.5. Methods Supplementary material 11 6. Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream Abstract 6.1. Background 6.2. Results 6.3. Discussion 6.4. Conclusions 6.5. Methods Supplementary Material 7. Diet and Host Genetics Drive the Bacterial and Fungal Intestinal Metatranscriptome of Gilthead Sea Bream Abstract 7.1. Introduction 7.2. Results 7.3. Discussion 7.4. Materials and Methods Supplementary Material 8. Genetics and Nutrition Drive the Gut Microbiota Succession and Host-Transcriptome Interactions through the Gilthead Sea Bream (Sparus aurata) Production Cycle Simple summary Abstract 8.1. Introduction 8.2. Materials and Methods 8.3. Results 8.4. Discussion 8.5. Conclusions Supplementary Material 9. Can the genetic background modulate the effects of feed additives? Answers from gut microbiome and transcriptome interactions in farmed gilthead sea bream (Sparus aurata) Abstract 9.1. Introduction 9.2. Materials and methods 9.3. Results 9.4. Discussion 9.5. Conclusions Supplementary Material 10. General Discussion 11. Conclusions(▲) Figure 1.2. Ongoing world main challenges affecting aquaculture and the ultimate goals needed to achieve by the sector. Sustainability and biotechnological, automation, and nutritional technological innovations are postulated as the mechanisms for the accomplishment of these goals, as well as to lead the greening of the aquaculture sector. (▲) Figure 1.4. Simplified scheme of the Gh/Igf endocrine axis controlling growth in teleost fish. Multiple hormonal and nutritional factors may promote (+) the production and/or influence (+/-) the activity of IGF-1. Negative feedback (-) by Igf1 inhibits growth hormone secretion by the pituitary. (▲) Figure 1.9. Overview of the main questions addressed by A genomics, B transcriptomics, epigenomics, and C microbiomics, the omics used in this PhD thesis, in aquaculture settings.Harnessing the potential of omics integration approaches, as well as applying their outcomes again to the aquaculture systems, emerge as a k...