Skip to main content
Article thumbnail
Location of Repository

QueTAL: A suite of tools to classify and compare TAL effectors functionally and phylogenetically

By Alvaro L. Pérez-Quintero, Léo Lamy, Jonathan Gordon, Aline Escalon, Sébastien Cunnac, Boris Szurek and Lionel Gagnevin

Abstract

Transcription Activator-Like (TAL) effectors from Xanthomonas plant pathogenic bacteria can bind to the promoter region of plant genes and induce their expression. DNA-binding specificity is governed by a central domain made of nearly identical repeats, each determining the recognition of one base pair via two amino acid residues (a.k.a. Repeat Variable Di-residue, or RVD). Knowing how TAL effectors differ from each other within and between strains would be useful to infer functional and evolutionary relationships, but their repetitive nature precludes reliable use of traditional alignment methods. The suite QueTAL was therefore developed to offer tailored tools for comparison of TAL effector genes. The program DisTAL considers each repeat as a unit, transforms a TAL effector sequence into a sequence of coded repeats and makes pair-wise alignments between these coded sequences to construct trees. The program FuncTAL is aimed at finding TAL effectors with similar DNA-binding capabilities. It calculates correlations between position weight matrices of potential target DNA sequence predicted from the RVD sequence, and builds trees based on these correlations. The programs accurately represented phylogenetic and functional relationships between TAL effectors using either simulated or literature-curated data. When using the programs on a large set of TAL effector sequences, the DisTAL tree largely reflected the expected species phylogeny. In contrast, FuncTAL showed that TAL effectors with similar binding capabilities can be found between phylogenetically distant taxa. This suite will help users to rapidly analyse any TAL effector genes of interest and compare them to other available TAL genes and should improve our understanding of TAL effectors evolution. It is available at http://bioinfo-web.mpl.ird.fr/cgi-bin2/quetal/quetal.cgi.(Résumé d'auteur

Topics: H20 - Maladies des plantes, F30 - Génétique et amélioration des plantes
Year: 2015
DOI identifier: 10.3389/fpls.2015.00545
OAI identifier: oai:agritrop.cirad.fr:577257
Provided by: Agritrop

Suggested articles


To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.