New insights into Transposable Elements from high quality genome sequences across diverse animals

New high quality genomes, together with faster whole genome alignment methods, have opened the possibility of identifying new transposable element (TE) families by their polymorphic character in different haplotypes, in contrast to previous methods based on repetitiveness, homology and structural features. In this work, divided in four sections, I show how we can leverage this capability and the availability of new genome assemblies to improve our knowledge about transposable elements and the roles that they play in genome evolution. In the first chapter I provide an introduction about the current state of the art of transposable element identification methods and a brief description about their classification and, in particular, their transposition mechanisms. In the second chapter I present a new method that I implemented in a tool, Pantera, to obtain transposable element libraries from pangenomes of different haplotypes. I show how Pantera compares to similar tools and I present results of its application to a diverse range of species. These include 404 species of Lepidoptera from the Darwin Tree of Life where we found new Maverick families in species where they had not been previously reported, and doubled the number of total Maverick elements so far included in public TE databases. In the third chapter I focus on the study of transposable elements in the haplochromine cichlid fish radiation of Lake Malawi, uncovering the large diversity of transposable elements present in these cichlids and how they manifest different patterns of activity in different populations and species. To conclude this chapter I discuss different theories about the role of TEs in the speciation of their host species in the light of the data obtained. In the fourth chapter I examine the potential role of TEs in the formation of centromeres in the haplochromine radiation. I identify a novel sequence in most of their centromeres, whose origin I hypothesize is from a non autonomous transposable element, and provide some hypotheses as to how it might have contributed to centromere formation and function, discussing the implications for our current understanding of this component of the genomes that is critical (in most species) for correct meiosis and mitosis. Altogether my work shows the value of a correct annotation of transposable elements in genomes and how we can take new approaches to identify TEs and derive new insights about their contribution to genome biology.

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2025

Author dc:creator

• Sierra Rodríguez, Pío Alberto

Advisor dc:contributor.advisor

• Durbin, richard

• Comparative genomics
• Transposable elements
• Pangenomes
• Centromeres
• Cichlids

Licence

• https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/d20441bb-05ae-4b59-8b66-ddd6ceb13feb/download
• https://creativecommons.org/licenses/by/4.0/

DOI dc:identifier.doi

https://doi.org/10.17863/CAM.119501

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/386166