Alienness - Rapid detection of candidate horizontal gene transfers across the tree of life

Alienness tool is developed at ISA (INRAE-UNS-CNRS) in Sophia Antipolis, France.
This work was carried out by Corinne Rancurel & Etienne Danchin.

Horizontal gene transfer (HGT) is the transmission of genetic material between species by ways other than direct (vertical) inheritance from parents to the offspring. HGT is recognized as a major evolutionary force in prokaryotes as it is involved, for example in acquisition of antibiotic resistance or pathogeny. HGT has long been overlooked and considered insignificant in eukaryotes. However, HGT have also played important roles in the evolutionary history and biology of these species, including animals (1). For example, HGT have contributed to the colonization of land by plants, in the emergence of plant parasitism in nematodes or in the development of capabilities like resistance to extreme temperatures or desiccation. Progress in genome sequencing technologies has allowed multiple animal genomes to be publicly released. Systematic searches for HGT events in the root-knot nematodes or in the bdeloid rotifer, have shown that between 3 and 9 % of protein-coding genes in these species were probably of foreign origin (2,3). However, in the absence of a user-friendly, rapid and publicly available tool to detect HGT events in any taxonomic group of interest, we still lack a global view of the prevalence of HGT across a tree of life. Here, we propose Alienness, a taxonomy-aware web application that parses BLAST results against public libraries to rapidly identify candidate HGT in a genome of interest. Alienness takes as input the result of a BLAST of a whole proteome of interest against any NCBI protein library. The user defines recipient (e.g. metazoan) and donor (e.g. bacteria, fungi) branches of interest in the NCBI taxonomy. Based on the best blast e-values of candidate donor and recipient taxa, Alienness calculates an Alien Index (AI) for each query protein. Our method uses the Alien Index metrics as described in (4) to detect a significant gap of magnitude in e-values between candidate donor and recipient taxa. An AI >0 indicates a better hit to candidate donor than recipient taxa and a possible HGT. Higher AI represent higher gap of e-values between candidate donor and recipient and a more likely HGT. We confirmed the accuracy of Alienness on phylogenetically confirmed HGT of non-metazoan origin in plant-parasitic nematodes. Alienness scans whole proteomes to rapidly identify possible HGT in any species of interest and thus fosters exploration of HGT more easily and largely across the tree of life.

• Rancurel Corinne, Legrand Ludovic, Danchin Etienne G.J. Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life. Genes. 8, 248 (2017). https://doi.org/10.3390/genes8100248