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Incidence of Genome Structure, DNA Asymmetry, and Cell Physiology on T-DNA Integration in Chromosomes of the Phytopathogenic Fungus Leptosphaeria maculans


Bourras, S; Meyer, M; Grandaubert, J; Lapalu, N; Fudal, I; Linglin, J; Ollivier, B; Blaise, F; Balesdent, M-H; Rouxel, T (2012). Incidence of Genome Structure, DNA Asymmetry, and Cell Physiology on T-DNA Integration in Chromosomes of the Phytopathogenic Fungus Leptosphaeria maculans. G3 : Genes, Genomes, Genetics, 2(8):891-904.

Abstract

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 com- partmentalized genome. A total of 318 T-DNA tags were recovered and analyzed for biases in chromo- some 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 tar- geted 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 micro- homologies 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.

Abstract

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 com- partmentalized genome. A total of 318 T-DNA tags were recovered and analyzed for biases in chromo- some 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 tar- geted 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 micro- homologies 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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Item Type:Journal Article, not refereed, original work
Communities & Collections:07 Faculty of Science > Department of Plant and Microbial Biology
Dewey Decimal Classification:580 Plants (Botany)
Language:English
Date:1 August 2012
Deposited On:28 Feb 2013 16:43
Last Modified:07 Dec 2017 20:28
Publisher:Genetics Society of America
ISSN:2160-1836
Publisher DOI:https://doi.org/10.1534/g3.112.002048

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