This Is AuburnElectronic Theses and Dissertations

Comparative analysis of repetitive elements in fish genomes




Yuan, Zihao

Type of Degree

PhD Dissertation


Fisheries and Allied Aquacultures


Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, this dissertation work focused on comparative analysis of repetitive elements presented in three chapters: general overview and literature review (Chapter 1), analysis and annotation of the repetitive elements in the channel catfish genome (Chapter 2), and comparative analysis of repetitive elements from a large number (52) of the fish genomes (Chapter 3) Channel catfish (Ictalurus punctatus) is a highly adaptive species and has been used as a research model for comparative immunology, physiology, and toxicology among ectothermic vertebrates. It is also economically important for the industry. As such, its reference genome was generated and annotated with protein coding genes. However, the repetitive elements in the catfish genome are less well understood. In this study, over 417.8 Megabase (MB) of repetitive elements were identified and characterized in the channel catfish genome. Among them, the DNA/TcMar-Tc1 transposable elements are the most abundant type, making up ~20% of the total repetitive elements, followed by the microsatellites (14%). The prevalent of repetitive elements, especially the mobile elements, may have provided a driving force for the evolution of the catfish genome. A number of catfish-specific repetitive elements were identified including the previously reported Xba elements whose divergence rate was relatively low, slower than that in untranslated regions of genes but faster than the protein coding sequences, suggesting its evolutionary restrictions. The content of the repetitive elements varies significantly among the fish genomes. To provide insights into the roles of repetitive elements in fish genomes, a comparative analysis of repetitive elements from all sequenced teleost fish genomes of 52 species in 22 orders was conducted. The proportions of repetitive elements in various genomes were found to be positively correlated with genome sizes, with a few exceptions. More importantly, specific enrichment appeared between some repetitive element categories with species habitats. Specifically, class II transposons appear to be more abundant in freshwater bony fishes than in marine bony fishes when the phylogeny is not considered. In contrast, marine bony fishes harbor more tandem repeats than freshwater species. In addition, class I transposable elements appear to be more abundant in primitive species, such as cartilaginous fish and lamprey than in bony fishes. The enriched association of specific categories of repetitive elements with fish habitats suggests the importance of repetitive elements in genome evolution and their potential roles in fish adaptation to their living environments.