Leveraging the dynamic repeat element landscape of squamate reptile genomes to understand broad patterns of Vertebrate genome evolution and transposable element biology

Abstract

Vertebrate genomes are mostly composed of transposable elements (TE), mobile DNA sequences that have shaped genome structure and evolution by promoting positive (e.g., regulatory network rewiring, embryo development) and negative (e.g., ectopic recombination, disease) genomic processes. Leveraging genomic and transcriptomic data from diverse vertebrate species, I present novel lines of evidence that underscore the unique value of squamate reptile genomes for investigating properties of TE landscape evolution. This dissertation demonstrates that squamate genomes defy paradigms of amniote repeat element evolution set by mammals and birds, in particular: that greater variability in TE content is found between major lineages, that genome size correlates to genomic TE content, and that effective population size relates to features of the TE landscape (i.e., full-length insertions and TE abundance). Squamates are also unique among amniotes for having a broad diversity of TE types and families that appear similarly prevalent in the genome and simultaneously active, whereas patterns of negative regulation of TEs in germline tissues are consistent with those of other vertebrate species (with the exception of mammals). The detailed investigation of the prairie rattlesnake genome further shows that TEs have been involved in sex chromosome evolution, gene duplication and isochore structure, demonstrating that the distinct evolutionary dynamics of squamate TE landscapes may be linked to more unique and variable aspects of squamate genome function and evolution compared to other amniote species.