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AnnoTALE - Identification, Annotation and Classification of Transcription Activator-Like Effectors
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Edité par CCSD -
International audience. Plant-pathogenic Xanthomonas bacteria use transcription activator-like effectors (TALEs) that bind to the promoter of plant genes and activate their transcription. Xanthomonas infections result in a substantial yield loss for many crop plants including rice. The binding domain of TALEs consists of tandem repeats containing two hypervariable amino acids, which are called repeat variable di-residue (RVD). Each RVD recognizes one nucleotide of its target DNA and the consecutive array of RVDs determines TALE target specificity.Here, we present AnnoTALE, an application for annotating TALEs in Xanthomonas genomes, for analyzing their structure, for clustering TALEs by the similarity of their RVD sequences, and for predicting putative TALE target genes. We sequence the genome of Xanthomonas oryzae pv. oryzae PXO83 by PacBio sequencing and use AnnoTALE to predict all TALE genes of this strain. Building classes of TALEs from published and the newly sequenced Xanthomonas genomes allows us to gain new insights into TALE evolution.We find that RVDs are highly conserved even on the codon level. We discover that only one to three codon pairs coding for one RVD occur in known TALEs, even though the number of theoretically possible codon pairs is substantially larger. In addition, some codon pairs found frequently in RVDs are rather rare in the remaining TALE sequence and in coding sequences of other genes.We compare the aligned RVDs of the class members and generate a network of possible and observed substitutions and find only one synonymous substitution between two codon pairs for RVD NN, whereas the remaining substitutions lead to a modification of the RVD. Most frequently, only one nucleotide is substituted between the compared RVDs of two class members. Our findings indicate that one way how TALE specificities evolve is by direct base substitutions in RVD codons.
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