# TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations

## TL;DR

TEPEAK is a new tool that helps scientists study jumping DNA in wild and under-researched animal populations, revealing genetic diversity and domestication effects.

## Contribution

TEPEAK introduces a novel framework for identifying transposable elements without prior genomic knowledge, enabling population-scale analysis in non-model species.

## Key findings

- Application to 257 horse genomes revealed population structure and domestication-driven changes in transposable element diversity.
- TE insertions overlapping genes related to behavior, muscle function, and neurological traits were identified.
- TEPEAK detected shared insertions in closely related equid species, showing evolutionary persistence of element families.

## Abstract

Transposable elements (TEs) replicate within genomes and are an active source of genetic variability in many species. Their role in immunity and domestication underscores their biological significance. However, analyzing TEs, especially within lesser-studied and wild populations, poses considerable challenges. To address this, we introduce TEPEAK, a simple and efficient approach to identify and characterize TEs in populations without any prior sequence or loci information. In addition to processing user-submitted genomes, TEPEAK integrates with the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) to increase cohort sizes or incorporate proximate species. Our application of TEPEAK to 257 horse genomes spanning 11 groups reaffirmed established genetic histories and highlighted disruptions in crucial genes. Some identified TEs were also detectable in species closely related to horses. TEPEAK paves the way for comprehensive genetic variation analysis in traditionally understudied populations by simplifying TE studies. TEPEAK is open-source and freely available at https://github.com/ryanlayerlab/TEPEAK.

Transposable elements are DNA sequences that can move within genomes and generate genetic diversity. Despite their importance for evolution and adaptation, they remain poorly characterized in many species, especially those without extensive genomic resources. We developed TEPEAK, an open-source framework that identifies and analyzes transposable elements across populations without needing prior knowledge of their sequences. TEPEAK detects insertion patterns shared among individuals, enabling large-scale comparisons of genome variation and its functional consequences.

We applied TEPEAK to 257 horse genomes spanning 11 populations to showcase its capabilities. Our results revealed clear population structure based on element insertions and showed that domestication and selective breeding have altered the diversity and frequency of these elements across breeds. We identified insertions overlapping genes related to behavior, muscle function, and neurological traits—features often targeted during domestication. By extending our analysis to closely related equids, we also traced the evolutionary persistence of several element families. TEPEAK provides an accessible approach for exploring how mobile DNA shapes population diversity, adaptation, and the genomic legacy of domestication.