Simulation based estimation of branching models for LTR retrotransposons

TL;DR

This paper introduces a simulation-based branching model for studying the propagation of LTR retrotransposons in genomes, accounting for positions, degradations, and variable duplication rates, with applications to Drosophila.

Contribution

It presents a novel branching model that incorporates positional and degradation factors for LTR retrotransposons, along with simulation and estimation tools.

Findings

Simulation tools enable accurate parameter estimation.

Applied to Drosophila, revealing transposable element spread patterns.

Open-source Python implementation available online.

Abstract

Motivation: LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows to take into account both positions and degradations of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. Results: Various functions have been implemented in order to simulate their spread and visualization tools are proposed. Based on these simulation tools, we show that an accurate estimation of the parameters of this propagation model can be performed. We applied this method to the study of the spread of the transposable elements ROO, GYPSY, and DM412 on a chromosome of \textit{Drosophila melanogaster}. Availability: Our proposal has been implemented using Python software. Source code is freely available on the web at https://github.com/SergeMOULIN/retrotransposons-spread.