Transposable element annotation for a Genome Assembly of the stalk-eyed fly, Teleopsis dalmanni

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Wilkinson, Gerald
Baker, Richard
Reinhardt, Josephine
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Stalk-eyed flies in the genus Teleopsis are known to carry selfish genetic elements that induce sex ratio (SR) meiotic drive and impact the fitness of male and female carriers. We have recently produced a chromosome-level genome assembly of the stalk-eyed fly, T. dalmanni, to elucidate the pattern of genomic divergence associated with the presence of drive elements. We find evidence for multiple nested inversions along the sex ratio haplotype and widespread differentiation and divergence between the inversion types along the entire X chromosome. We also find that the genome contains tens of thousands of transposable element (TE) insertions and hundreds of transcriptionally active TE families producing new insertions. Moreover, we find evidence that many TE families are expressed at a significantly higher level in SR male testis, suggesting a genetic connection between these two types of selfish genetic elements in this species. This file contains the DNA sequences of the transposable elements discussed in this study.
Consensus fasta sequences of transposable elements annotated from the T. dalmanni ss NLCU01 v. 1.0 genome assembly (BioProject: PRJNA391339) using RepeatModeler v 1.0.4 (Smit and Hubley 2008) with default parameters. Smit, A., and R. Hubley. 2008. RepeatModeler Open-1.0.