title: AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences.
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.
authors.affiliation: Institute of Computer Science, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Grau
authors.affiliation: Department of Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, D-06120 Halle (Saale), Germany.|Department of Plant Biotechnology, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany.
authors.forename: Maik
authors.initials: M
authors.lastname: Reschke
authors.affiliation: Institute of Computer Science, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany.
authors.forename: Annett
authors.initials: A
authors.lastname: Erkes
authors.affiliation: Department of Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, D-06120 Halle (Saale), Germany.|Department of Plant Biotechnology, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany.
authors.forename: Jana
authors.initials: J
authors.lastname: Streubel
authors.affiliation: New England Biolabs Inc., 240 Country Road, Ipswich, MA 01938, USA.
authors.forename: Richard D
authors.initials: RD
authors.lastname: Morgan
authors.affiliation: New England Biolabs Inc., 240 Country Road, Ipswich, MA 01938, USA.
authors.forename: Geoffrey G
authors.initials: GG
authors.lastname: Wilson
authors.affiliation: IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME) 34394 Montpellier France.
authors.forename: Ralf
authors.initials: R
authors.lastname: Koebnik
authors.affiliation: Department of Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, D-06120 Halle (Saale), Germany.|Department of Plant Biotechnology, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Boch
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D019295:Computational Biology; D019143:Evolution, Molecular; D016678:Genome; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA; D000071336:Transcription Activator-Like Effectors / Q000235:genetics*; D037521:Virulence Factors / Q000235:genetics; D014974:Xanthomonas / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D000071336:Transcription Activator-Like Effectors; D037521:Virulence Factors