Exploring the Extent, Routes and Fate of Horizontal Transfers In Plant Nuclear Genomes – EXOTICA

Horizontal Transfers (HTs) refers to the movement of genetic material between distantly related species by mechanisms other than sexual reproduction. In prokaryotes, HTs are well known to be a source of new adaptive traits such as the spreading of genes implicated in antibiotic resistance. Over the last decade, it has become increasingly obvious that in eukaryotes too such as plants, HTs can also lead to major evolutionary leaps and very fast adaptation to new ecological niches that would not be possible only by standard genetic mutations. However, little is known about their rate, evolutionary significance and the biotic interaction promoting HT between plants. While host-parasite relationships appear to be a major pathway for horizontal transfers, an increasing number of HT cases reported in recent years involve species that do not share intimate cell-to-cell contact. This, raises the question alternative HT pathway between species not involved in tight physical contact and the possible involvement of vectors.
With the advent of next and third generation sequencing technologies and the substantial increase of genomic data in plants, it becomes feasible to assess the extent and routes of HT at an unprecedented larger-scale. While these sequencing technologies have enabled a massive increase in genomic data from plants and other organisms, new challenges must be addressed not only in terms of bioinformatics analysis of large datasets, but also for the automatic and accurate HT characterization. To date, no studies have been conducted on a genome-wide scale and for a large number of plant species. Indeed, most previous HT studies have focused on specific genes or only on certain transposable elements (TEs) classes and on a limited number of plant species.
The EXOTICA project seeks to tackle those challenges by providing innovative comparative genomic approaches for HTs characterization that could handle big genomic data in order to determine the extent, possible routes and the nature of biological interactions promoting HTs in plants. We have recently developed novel bioinformatics approaches that seek to characterize HTs at the whole genome scale and without any prior knowledge on genome annotation. Thanks to these tools, we will characterize HTs on an unprecedented scale by comparing thousands of publicly available genomes and by de novo sequencing of several plant species from a natural ecosystem: the Massane forest located in southern France. EXOTICA will set up the basis for a full and comprehensive understanding of HT routes and the type of biotic interactions promoting HT between non-parasitic plants. We will also test the hypothesis of the implication of vector such as bacteria, fungi or insect in plant-to-plant DNA transfer.