Preprint Technical Note Version 1 This version not peer reviewed

Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

Version 1 : Received: 31 August 2017 / Approved: 31 August 2017 / Online: 31 August 2017 (15:03:30 CEST)

A peer-reviewed article of this Preprint also exists.

Rancurel, C.; Legrand, L.; Danchin, E.G.J. Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life. Genes 2017, 8, 248. Rancurel, C.; Legrand, L.; Danchin, E.G.J. Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life. Genes 2017, 8, 248.

Journal reference: Genes 2017, 8, 248
DOI: 10.3390/genes8100248

Abstract

Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in metazoan. Here, we propose Alienness, a taxonomy-aware web application that parses BLAST results against public libraries to rapidly identify candidate HGT in any 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. 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.

Subject Areas

horizontal gene transfer; alien index; lateral gene transfer

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