Details
| Original language | English |
|---|---|
| Article number | 21077 |
| Journal | Scientific Reports |
| Volume | 6 |
| Publication status | Published - 15 Feb 2016 |
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.
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In: Scientific Reports, Vol. 6, 21077, 15.02.2016.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences
AU - Grau, Jan
AU - Reschke, Maik
AU - Erkes, Annett
AU - Streubel, Jana
AU - Morgan, Richard D.
AU - Wilson, Geoffrey G.
AU - Koebnik, Ralf
AU - Boch, Jens
N1 - Funding Information: This work was supported by grants from the Deutsche Forschungsgemeinschaft (BO 1496/8-1 to JB and GR 4587/1-1 to JG) and a grant from the European Regional Development Fund of the European Commission to JB and by the COST action FA1208 “SUSTAIN”. The authors thank Carola Kretschmer for technical assistance, Romina Plötner for infection studies, Ulla Bonas for support, and Stefan Posch for valuable discussions. Publisher Copyright: © 2016, Nature Publishing Group. All rights reserved. Copyright: Copyright 2018 Elsevier B.V., All rights reserved.
PY - 2016/2/15
Y1 - 2016/2/15
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84958213523&partnerID=8YFLogxK
U2 - 10.1038/srep21077
DO - 10.1038/srep21077
M3 - Article
C2 - 26876161
AN - SCOPUS:84958213523
VL - 6
JO - Scientific Reports
JF - Scientific Reports
SN - 2045-2322
M1 - 21077
ER -