DaTALbase : a database for genomic and transcriptomic data related to TAL effectors

2018

Article référencé dans le Web of Science WOS:000427306500007

Perez-Quintero A. L., Lamy Léo, Zarate C. A., Cunnac Sébastien, Doyle E., Bogdanove A., Szurek Boris, Dereeper Alexis

Molecular Plant-Microbe Interactions, 2018, 31 (4), p. 471-480 ISSN 0894-0282

Transcription activator-like effectors (TALEs) are proteins found in the genus Xanthomonas of phytopathogenic bacteria. These proteins enter the nucleus of cells in the host plant and can induce the expression of susceptibility genes (S genes), triggering disease. TALEs bind the promoter region of S genes following a specific code, which allows the prediction of binding sites based on TALEs amino acid sequences. New candidate S genes can then be discovered by finding the intersection between genes induced in the presence of TALEs and genes containing predicted effector binding elements. By contrasting differential expression data and binding site predictions across different datasets, patterns of TALE diversification or convergence may be unveiled, but this requires the seamless integration of different genomic and transcriptomic data. With this in mind, we present daTALbase, a curated relational database that integrates TALE-related data including bacterial TALE sequences, plant promoter sequences, predicted TALE binding sites, transcriptomic data of host plants in response to TALE-harboring bacteria, and other associated data. The database can be explored to uncover new candidate S genes as well as to study variation in TALE repertories and their corresponding targets. The first version of the database here presented includes data for Oryza sp.-Xanthomonas pv. oryzae interactions. Future versions of the database will incorporate information for other pathosystems involving TALEs.

Sciences fondamentales / Techniques d'analyse et de recherche [020] ; Sciences du monde végétal [076] ; Biotechnologies [084]

Fonds IRD [F B010072484]

fdi:010072484