Transposable elements in teleost fish: In silico exploration of TE activity, diversity and abundance across 74 teleost fish genomes
Transposable elements (TEs) comprise a major proportion of most large eukaryotic genomes. Through different mechanisms of transposition, TEs can move within genomes and cause genomic rearrangements. Large-scale studies of TEs have recently become possible through the advent of high-throughput sequen...
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| Format: | Master Thesis |
| Language: | English |
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2016
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| Online Access: | http://hdl.handle.net/10852/52365 http://urn.nb.no/URN:NBN:no-55565 |
| Summary: | Transposable elements (TEs) comprise a major proportion of most large eukaryotic genomes. Through different mechanisms of transposition, TEs can move within genomes and cause genomic rearrangements. Large-scale studies of TEs have recently become possible through the advent of high-throughput sequencing. Thus, unprecedented opportunities for uncovering the TE compositions in genomes from a vast range of species have presented itself. Teleost fish are an infraclass within ray-finned fishes, with a long evolutionary history, that display vast diversity in morphology and a variety of life history strategies. Compared with other vertebrates, the genomes of teleost fish have been shown to inhabit a highly diverse composition of TEs, many of which show signs of recent activity. In addition, the link between genome size and TE abundances has been indicated to be particularly strong. However, less than 20 different teleost fish have so far been analyzed with regard to TE content. Using nine available and 65 newly sequenced teleost genome assemblies, this project aimed to explore TE diversity, abundance and activities within teleost fish genomes. A custom computational pipeline was devised to annotate the genomes of 74 different teleostean species, including a more extensive investigation of a recently improved version of the Atlantic cod genome. Results were coupled to a time-calibrated phylogenetic tree for an investigation of the TE data in a proper evolutionary context. The study revealed a substantial variation in TE content and that the variation mostly follows phylogenetic patterns. Unique in scale, this study uncovers that i) DNA transposons are predominant TEs, ii) the diversity of TE superfamilies/families is high and iii) that recent TE activity is common in teleost fish. In addition, an investigation of TE activity over time revealed the presence of a strong phylogenetic signal present in the repeat landscapes of genomes that diverged less than 20 million years ago. Last, a strong correlation between genome size and TE abundance are indicated. |
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