Towards an accurate identification of partial horizontal gene transfers and intragenic recombination

Authors : Alix Boc and Vladimir Makarenkov

Abstract

A common way for Bacteria and Archae to adapt to different environmental conditions is via the acquisition of mosaic genes. A mosaic gene is composed of sequence polymorphisms identical to the recipient original allele in some parts of the gene but derived from the integrated DNA in the other parts. Usually, the integrated sequence contains a selectable genetic marker (e.g., marker allowing for antibiotic resistance). An effective identification of mosaic genes and validation of corresponding partial horizontal gene transfer (HGT) is one of the major challenges in the evolutionary biology. We developed a method for detecting partial HGT events and the related intragenic recombination. A bootstrap procedure incorporated in our method is used to assess the support of each predicted partial gene transfer. The proposed method can be also employed to confirm or discard complete (i.e., traditional) gene transfers detected by any HGT inferring method. When applied on a full-genome scale, the new method can be useful to assess the rates of complete and partial gene transfer underlying the evolution of considered organisms.

Link to paper on Nucleic Acids Research

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Newick Builder

Je viens de mettre en ligne la première version (0.1) de Newick Builder. Il s’agit d’un utilitaire écrit en Javascript qui permet de générer le format Newick d’un arbre dessiné sur un <canvas>.

Pour le moment, c’est une application assez basique, qui se veut volontairement simple. Vous devez dessiner votre arbre phylogénétique sur le <canvas>.  Plusieurs options sont disponibles comme la suppression et le déplacement de branches, l’édition du nom des feuilles etc… Plusieurs améliorations seront apportées avec le temps.