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

作者：Grau Jan; Reschke Maik; Erkes Annett; Streubel Jana; Morgan Richard D; Wilson Geoffrey G; Koebnik Ralf; Boch Jens

来源：Scientific Reports, 2016, 6(1): 21077.

DOI：10.1038/srep21077

<jats:title>Abstract</jats:title><jats:p>Transcription activator-like effectors (TALEs) are virulence factors, produced by the bacterial plant-pathogen <jats:italic>Xanthomonas</jats:italic>, 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 <jats:italic>Xanthomonas</jats:italic> 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 <jats:italic>TALE</jats:italic> genes by the use of PacBio sequencing. We present ‘AnnoTALE’, a suite of applications for the analysis and annotation of <jats:italic>TALE</jats:italic> genes from <jats:italic>Xanthomonas</jats:italic> genomes and for grouping similar TALEs into classes. Based on these classes, we propose a unified nomenclature for <jats:italic>Xanthomonas</jats:italic> 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.</jats:p>

• 出版日期2016-2-15