AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences

authored by

Jan Grau, Maik Reschke, Annett Erkes, Jana Streubel, Richard D. Morgan, Geoffrey G. Wilson, Ralf Koebnik, Jens Boch

Abstract

Transcription activator-like effectors (TALEs) are virulence factors, produced by the bacterial plant-pathogen Xanthomonas, that function as gene activators inside plant cells. Although the contribution of individual TALEs to infectivity has been shown, the specific roles of most TALEs, and the overall TALE diversity in Xanthomonas spp. is not known. TALEs possess a highly repetitive DNA-binding domain, which is notoriously difficult to sequence. Here, we describe an improved method for characterizing TALE genes by the use of PacBio sequencing. We present 'AnnoTALE', a suite of applications for the analysis and annotation of TALE genes from Xanthomonas genomes, and for grouping similar TALEs into classes. Based on these classes, we propose a unified nomenclature for Xanthomonas TALEs that reveals similarities pointing to related functionalities. This new classification enables us to compare related TALEs and to identify base substitutions responsible for the evolution of TALE specificities.

Organisation(s)

Section Plant Biotechnology

External Organisation(s)

Martin Luther University Halle-Wittenberg
New England Biolabs
Université Montpellier

Type

Article

Journal

Scientific Reports

Volume

6

ISSN

2045-2322

Publication date

15.02.2016

Publication status

Published

Peer reviewed

Yes

ASJC Scopus subject areas

General

Electronic version(s)

https://doi.org/10.1038/srep21077 (Access: Open)