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daTALbase: A Database for Genomic and Transcriptomic Data Related to TAL Effectors.

Alvaro L Pérez-Quintero1,2, Léo Lamy1, Carlos A Zarate1

  • 11 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France.

Molecular Plant-Microbe Interactions : MPMI
|November 17, 2017
PubMed
Summary
This summary is machine-generated.

Researchers developed daTALbase, a database integrating TALE protein sequences, plant gene data, and transcriptomic information. This resource aids in discovering new plant susceptibility genes and understanding TALE evolution in plant pathogens.

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Area of Science:

  • Plant Pathology
  • Microbial Genetics
  • Bioinformatics

Background:

  • Transcription activator-like effectors (TALEs) from Xanthomonas bacteria induce plant disease by activating susceptibility (S) genes.
  • TALE binding to plant gene promoters follows a predictable code, enabling identification of potential S genes.
  • Integrating diverse genomic and transcriptomic data is crucial for studying TALE-plant interactions and evolution.

Purpose of the Study:

  • To present daTALbase, a curated relational database for TALE-related data.
  • To facilitate the discovery of novel plant S genes.
  • To enable the study of TALE diversification and convergence across different plant-pathogen systems.

Main Methods:

  • Compilation of bacterial TALE sequences and plant promoter sequences.
  • Prediction of TALE binding sites using TALE amino acid sequences.
  • Integration of transcriptomic data from host plants responding to TALE-harboring bacteria.
  • Development of a relational database (daTALbase) to store and query integrated data.

Main Results:

  • daTALbase successfully integrates TALE sequences, plant promoter data, predicted binding sites, and transcriptomic profiles.
  • The database structure allows for the identification of candidate S genes by intersecting induced genes with predicted TALE targets.
  • The initial version focuses on the Oryza sp.-Xanthomonas pv. oryzae pathosystem, with plans for expansion.

Conclusions:

  • daTALbase provides a valuable resource for researchers studying TALE-mediated plant pathogenesis.
  • The database supports the discovery of new S genes and the investigation of TALE evolution.
  • Future versions will broaden the scope to include additional plant-pathogen interactions involving TALEs.