Fishing for Junk: investigating the genomic and evolutionary roles of transposable element expansion within neotropical catfish

Butler, Christopher (2022) Fishing for Junk: investigating the genomic and evolutionary roles of transposable element expansion within neotropical catfish. Doctoral thesis, University of East Anglia.

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Transposable elements (TEs) are short DNA sequences that possess the ability to replicate throughout a genome. They are found ubiquitously across the tree of life and can reach high genomic abundance. Understanding the evolutionary and genomic consequences of TE action is thus of great importance and is aided by a growing ability to annotate TEs within non-model organisms. Teleost genomes have the greatest diversity of TEs of any vertebrate and are therefore ideal study systems to better understand TE biology. This work presents the first detailed foray into the TE biology of the Corydoradinae, a species rich clade of Neotropical catfish with an evolutionary history characterised by rapid colour pattern change, polyploidy and TE proliferation. In-silico modelling was utilised to demonstrate that TE proliferations may be driven by both beneficial insertion effects and whole genome duplications. The latest ‘de-novo’ TE pipelines were utilised to create a Corydoradinae-specific TE library, with this process increasing estimated TE abundance, altering TE composition, and reducing approximate age of insertions. A significant phylogenetic shift in expressed TE content within the Corydoradinae is also found, though this is somewhat dependent on choice of TE library during annotation. Furthermore, TE insertions appear to accumulate in genic regions at a greater rate within polyploid versus non-polyploid species. For example, a Mariner TE with an amphibian origin has horizontally transferred and inserted within the bone developmental gene ‘mmp13’ of multiple polyploid Corydoradinae species, with potential impacts regarding facial shape diversification. Finally, despite many incidences of TE activity inducing changes to colour pattern phenotypes in other organisms, Corydoradinae pigmentation genes were not found to be enriched in TE insertions and evolve under stricter purifying selection pressure than other genes. In summary, this work furthers our understanding of the causes and consequences of TE activity within a non-model system.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Biological Sciences
Depositing User: Chris White
Date Deposited: 21 Mar 2023 08:25
Last Modified: 21 Mar 2023 08:25


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