Evolution and diversity of transposable elements in vertebrate genomes

Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, were view the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4-60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds andmammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led tomisleading conclusions about genome evolution. Finally, recent advances inlong-read sequencing will soon permit access to TErich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes.