What do I do ?

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.

References
1. E.G.J. Danchin. Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube? BMC Biology (2016). (View Online)
2. J. Paganini et al. Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes. PLoS One (2012). (View online)
3. J.-F. Flot et al., Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga, Nature (2013). (View Online)
4. E. A. Gladyshev, et al., Massive horizontal gene transfer in bdelloid rotifers, Science (2008). (View Online)

What's news ?

1st December 2020

AvP : Alienness versus Predictor

Phylogenetic analysis is necessary to more robustly confirm HGT candidates. Also, alienness team present AvP ( Alienness versus Predictor) to automatically detect candidate HGTs within a phylogenetic framework. It is accessible under GNU General PublicLicense v3.0 at https://github.com/GDKO/AvP pending the implementation of the AvP module in the Alienness web server. AI features file is necessary to use AvP. This file is now available in the result archive of the alienness tool.

Update version 2.0

Using Accession.version Numbers instead of GI Numbers
NCBI is in the process of changing the way we handle GI numbers for sequence records. As part of this transition, we have make appropriate updates. The new version of Alienness henceforth uses output blast or diamond formats where each line contains the accession.version instead of gi.
More input formats accepted
Now, you can provide outformat six or seven for blast tool, or standard output of diamond.
Calculation of the HGT index
In addition to the Alien Index (AI), the HGT index is calculated.
Supporting donors
This version of Alienness evaluates the number of donor hits that supports the detected HGT taxon for each queries.
Visual exploration of blast results
Alienness offers an html index that allows visual exploration of the blast results, in particular by means of color coding. The novelty lies in the comparison of each lineage of hits following the donor to the donor's lineage. These hits are grouped together as long as they share the same node with the donor. Each button contains the lineage shared with the donor.

More information

Date of taxonomy update

Alienness release
2020-12-01
Latest ncbi session
2020-11-27

Example of results

Alienness_dataset_result.zip
Proteome
Meloidogyne incognita
Taxonomic group of interest
Metazoa 33208
Taxon group(s) to exclude
Tylenchomorpha 33283

Dataset Download

Alienness_dataset.zip
blast output: 32 queries of
Meloidogyne incognita
You can test with :
Taxonomic group of interest
Metazoa 33208
Taxon group(s) to exclude
Tylenchomorpha 33283

POSTER & PUBLICATION

POSTER ECCB 2014
Alienness: Rapid detection of horizontal gene transfers in metazoan genomes
(View Online)
PUBLICATION
Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life.
Genes 2017, 8(10), 248;
(View Online)