Horizontal transfers of transposable elements: What makes genome invasions successful? – TranspHorizon

In a first package, we will collect about 99 different insect species from 10 different collecting sites all over the world. Genomic DNAs will be extracted and sequenced using the nanopore technology. HTT events between these 99 species will be inferred and we will assess the role of sympatry and geographic distance on the success of HTTs in a robust statistical framework. We will also experimentally mimic horizontal transfers of chosen TEs into various species of Drosophila, showing different degrees of phylogenetic relatedness with D. melanogaster. Transposable elements from D. melanogaster will be introduced in foreign species by CRISPR-Cas9 technology. The rate of successful invasion and the dynamics of the elements will be monitored in each population raised under identical conditions using real-time PCR. In a second package, we will couple experimental populations of D. melanogaster (experiencing newly introduce TE amplification) with modeling and computer simulations. Active TEs will be selected from D. ananassae, and introduced by CRISPR-Cas9 in D. melanogaster. Experimental populations will be initialized by bringing few migrant flies with the TE into a naïve recipient population. The amplification dynamics (copy number, insertion site) and the genome regulation set-up will be monitored in each population, through regular DNA and RNA sequencing, and qPCR. Different conditions will be tested (population size, generation time, type of elements, interaction between several TEs). We propose to model the evolution of the transposition rate of an invading TE by taking into consideration the biological mechanisms of TE regulation. Implementation of the model will be done through mathematical difference equations and an individual-based simulation program. An ABC procedure will be used for confrontation of the model with the experimental data.

Insect collection is ongoing. We have already sequenced and assembled 18 species, and the statistical method for estimating the HTT frequency has been validated on another dataset. For experimental approaches, we have first identified potential active TE candidates, through lab experiment or population analysis of TE polymorphism. Some of these TEs have been introduced in D. melanogaster and we are monitoring the copy number increase. We have developed a model for the dynamics of TEs in populations. The model has been implemented in a simulation program, which will allow to identify the more relevant parameters for TE amplification.

Genome comparisons will allow the estimation of HTT frequency in the wild, and the influences of geographic locations and phylogenetic distances on this frequency. The monitoring of TEs amplification in experimental populations will allow to determine populational parameters influencing the amplification dynamics of TEs entering a new species..

Zhang H.-H., Peccoud J., Xu M.-R.-X., Zhang X-.G.,Gilbert C. Horizontal transfer and evolution of transposable elements in vertebrates. 2020. Nature Communications. 11:1362. doi.org/10.1038/s41467-020-15149-4

Transposable elements (TEs) are ubiquitous, mobile and repeated DNA sequences, having a major impact on genome evolution. However, many questions regarding their origin, diversity and dynamics remain unanswered. Horizontal transfer of TEs (HTTs), i.e. the passage of TEs between organisms without reproduction, is increasingly recognized as an important mechanism for shaping TE landscape. Yet to be successful, HTT also requires efficient subsequent amplification in the new host, which can be impaired by host silencing process or other species-specific factors. Our recent work have shown that i) HTT instances between insects are much more frequent than previously thought, ii) TE invasion of the host population and of the genome after a mimicked HTT is efficient, but is strongly affected by interactions between TE copies. Yet, the factors shaping global HTT trends remain poorly understood. The TranspHorizon project aims to evaluate the importance of five types of factors that may favor HTT or affect the success of post-HT TE amplification:
1- Host geographic and phylogenetic distances
Sympatric species are more likely to be ecologically connected than species living far apart from each other. Thus, we expect the number of HTT events to increase when the geographic distance decreases between populations. Conversely, compatibility between TEs and recipient host cells may decrease with the genetic distance from source lineages. Hence, HTT success should increase as the phylogenetic distance between species decreases.
2- Host species features
TE content varies substantially among species, both in terms of quantity (fraction of the genome derived from TE sequences) and quality (relative proportion of various TE families). Demographic and life-history traits (for example population size or mean generation time) could partly explain some of those variations.
3- TE features
TEs rely on either copy-and-paste or cut-and-paste mechanisms to transpose. Furthermore, TEs can also differ by their requirement for host factors, their ability to transfer easily from cell to cell, their propensity to insert in specific genome regions (such as regulatory piRNA clusters). We predict that these differences in transposition mechanism should impact HTT success in various ways.
4- Other elements and endosymbionts
The dynamics, activity, and interactions among TE families have often been compared to that of species in ecosystems. It has been shown experimentally that there were very strong interactions between autonomous and related non-autonomous TE copies, but we do not know whether the transposition dynamics is also influenced by the presence of unrelated TEs, or of non-TE parasites, such as the intracellular Wolbachia bacteria.
5- Emergence of the anti-TE immunity pathways
piRNA clusters are genomic loci enriched in TE sequences, which produce small RNAs able to silence TEs. Composition of piRNA clusters is highly variable among populations of the same species. piRNA clusters can be viewed as TE traps that will start regulating transposition as soon as a copy has jumped into. The time necessary for the piRNA pathway to efficiently silence an incoming TE is then likely dependent on the probability of this TE to jump into a piRNA cluster, which in turn depends on the transposition rate and on the size of the clusters relative to the size of the host genome.
In this project, we will combine approaches from ecology, field sampling, molecular biology, genome sequencing, bioinformatics, mathematics, and experimental evolution to address these questions, in two complementary work packages (WP). In WP1, we will assess how both phylogenetic and geographic distances affect the likelihood of HTT between insect species. In WP2, we will characterize both empirically and theoretically, the post-HTT amplification dynamics (copy number, and insertion frequency spectrum) and monitor the emergence of silencing, for various TEs, and in various population conditions.