Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae

(A) under bar grobacterium (t) under bar umefaciens-(m) under bar ediated (t) under bar ransformation ( ATMT) has become a prevalent tool for functional genomics of fungi, but our understanding of T-DNA integration into the fungal genome remains limited relative to that in plants. Using a model plant-pathogenic fungus, Magnaporthe oryzae, here we report the most comprehensive analysis of T- DNA integration events in fungi and the development of an informatics infrastructure, termed a (T) under bar -DNA (a) under bar nalysis (p) under bar latform (TAP). We identified a total of 1110 (T) under bar -DNA-(t) under bar agged (l) under bar ocations (TTLs) and processed the resulting data via TAP. Analysis of the TTLs showed that T- DNA integration was biased among chromosomes and preferred the promoter region of genes. In addition, irregular patterns of T- DNA integration, such as chromosomal rearrangement and readthrough of plasmid vectors, were also observed, showing that T- DNA integration patterns into the fungal genome are as diverse as those of their plant counterparts. However, overall the observed junction structures between T- DNA borders and flanking genomic DNA sequences revealed that T- DNA integration into the fungal genome was more canonical than those observed in plants. Our results support the potential of ATMT as a tool for functional genomics of fungi and show that the TAP is an effective informatics platform for handling data from large-scale insertional mutagenesis.