Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae.
Agrobacterium tumefaciens-mediated transformation (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-DNA analysis platform (TAP). We identified a total of 1110 T-DNA-tagged locations (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.
Choi
Jaehyuk
J
Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, Korea.
Park
Jongsun
J
Jeon
Junhyun
J
Chi
Myoung-Hwan
MH
Goh
Jaeduk
J
Yoo
Sung-Yong
SY
Park
Jaejin
J
Jung
Kyongyong
K
Kim
Hyojeong
H
Park
Sook-Young
SY
Rho
Hee-Sool
HS
Kim
Soonok
S
Kim
Byeong Ryun
BR
Han
Seong-Sook
SS
Kang
Seogchan
S
Lee
Yong-Hwan
YH
D016960:Agrobacterium tumefaciens / Q000235:genetics; D015825:Chromosomes, Fungal / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics*; D005822:Genetic Vectors / Q000235:genetics; D016681:Genome, Fungal; D020082:Magnaporthe / Q000235:genetics*; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D014170:Transformation, Genetic
D004269:DNA, Bacterial; C036483:T-DNA