Incidence of Genome Structure, DNA Asymmetry, and Cell Physiology on T-DNA Integration in Chromosomes of the Phytopathogenic Fungus Leptosphaeria maculans
2012
Bourras , Ahmed Salim (INRA , Thiverval-Grignon (France). UR 1290 BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes) | Meyer , Michel (INRA , Thiverval-Grignon (France). UR 1290 BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes) | Grandaubert , Jonathan (INRA , Thiverval-Grignon (France). UR 1290 BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes) | Lapalu , Nicolas (INRA , Thiverval-Grignon (France). UR 1290 BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes) | Fudal , Isabelle (INRA , Thiverval-Grignon (France). UR 1290 BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes) | LINGLIN , Juliette (INRA , Thiverval-Grignon (France). UR 1290 BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes) | Ollivier , Bénédicte (INRA , Thiverval-Grignon (France). UR 1290 BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes) | Blaise , Francoise (INRA , Thiverval-Grignon (France). UR 1290 BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes) | Balesdent , Marie-Helene (INRA , Thiverval-Grignon (France). UR 1290 BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes) | Rouxel , Thierry (INRA , Thiverval-Grignon (France). UR 1290 BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes)
The ever-increasing generation of sequence data is accompanied by unsatisfactory functional annotation, and complex genomes, such as those of plants and filamentous fungi, show a large number of genes with no predicted or known function. For functional annotation of unknown or hypothetical genes, the production of collections of mutants using Agrobacterium tumefaciens-mediated transformation (ATMT) associated with genotyping and phenotyping has gained wide acceptance. ATMT is also widely used to identify pathogenicity determinants in pathogenic fungi. A systematic analysis of T-DNA borders was performed in an ATMT-mutagenized collection of the phytopathogenic fungus Leptosphaeria maculans to evaluate the features of T-DNA integration in its particular transposable element-rich compartmentalized genome. A total of 318 T-DNA tags were recovered and analyzed for biases in chromosome and genic compartments, existence of CG/AT skews at the insertion site, and occurrence of microhomologies between the T-DNA left border (LB) and the target sequence. Functional annotation of targeted genes was done using the Gene Ontology annotation. The T-DNA integration mainly targeted gene-rich, transcriptionally active regions, and it favored biological processes consistent with the physiological status of a germinating spore. T-DNA integration was strongly biased toward regulatory regions, and mainly promoters. Consistent with the T-DNA intranuclear-targeting model, the density of T-DNA insertion correlated with CG skew near the transcription initiation site. The existence of microhomologies between promoter sequences and the T-DNA LB flanking sequence was also consistent with T-DNA integration to host DNA mediated by homologous recombination based on the microhomology-mediated end-joining pathway.
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