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

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

in 45/43 / 631/114/2184 / 631/208/212 / 631/326/421 / Agricultural production / Amino acids / Bacterial Proteins - genetics / Bioinformatics / Cloning / Computational Biology / Evolution, Molecular / Genome / Genomes / Humanities and Social Sciences / Infectivity / Life Sciences / Molecular Sequence Annotation / multidisciplinary / Nucleotide sequence / Pathogens / Plant cells / Science / Sequence Analysis, DNA / Transcription / Transcription Activator-Like Effectors - genetics / Virulence / Virulence factors / Virulence Factors - genetics / Xanthomonas - genetics

2016

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

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

2016

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

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

2016

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Journal Article

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

Koebnik, Ralf,

Morgan, Richard D.,

Streubel, Jana,

Boch, Jens,

Erkes, Annett,

Reschke, Maik,

Wilson, Geoffrey G.,

Grau, Jan

2016

Overview

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.

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Publisher

Nature Publishing Group UK,Nature Publishing Group

Subject

/ Agricultural production

/ Amino acids

/ Bacterial Proteins - genetics