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

Jaehyuk Choi, Jongsun Park, Junhyun Jeon, Myoung Hwan Chi, Jaeduk Goh, Sung Yong Yoo, Jaejin Park, Kyongyong Jung, Hyojeong Kim, Sook Young Park, Hee Sool Rho, Soonok Kim, Byeong Ryun Kim, Seong Sook Han, Seogchan Kang, Yong Hwan Lee

Research output: Contribution to journalArticle

56 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)371-382
Number of pages12
JournalMolecular Microbiology
Volume66
Issue number2
DOIs
StatePublished - Oct 1 2007

Fingerprint

Magnaporthe
Chromosomes
Genome
Fungal Genome
Fungi
Agrobacterium tumefaciens
Informatics
Genomics
Oryza
T-DNA
Insertional Mutagenesis
Genetic Promoter Regions

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Molecular Biology

Cite this

Choi, J., Park, J., Jeon, J., Chi, M. H., Goh, J., Yoo, S. Y., ... Lee, Y. H. (2007). Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae. Molecular Microbiology, 66(2), 371-382. https://doi.org/10.1111/j.1365-2958.2007.05918.x
Choi, Jaehyuk ; Park, Jongsun ; Jeon, Junhyun ; Chi, Myoung Hwan ; Goh, Jaeduk ; Yoo, Sung Yong ; Park, Jaejin ; Jung, Kyongyong ; Kim, Hyojeong ; Park, Sook Young ; Rho, Hee Sool ; Kim, Soonok ; Kim, Byeong Ryun ; Han, Seong Sook ; Kang, Seogchan ; Lee, Yong Hwan. / Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae. In: Molecular Microbiology. 2007 ; Vol. 66, No. 2. pp. 371-382.
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abstract = "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.",
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Choi, J, Park, J, Jeon, J, Chi, MH, Goh, J, Yoo, SY, Park, J, Jung, K, Kim, H, Park, SY, Rho, HS, Kim, S, Kim, BR, Han, SS, Kang, S & Lee, YH 2007, 'Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae', Molecular Microbiology, vol. 66, no. 2, pp. 371-382. https://doi.org/10.1111/j.1365-2958.2007.05918.x

Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae. / Choi, Jaehyuk; Park, Jongsun; Jeon, Junhyun; Chi, Myoung Hwan; Goh, Jaeduk; Yoo, Sung Yong; Park, Jaejin; Jung, Kyongyong; Kim, Hyojeong; Park, Sook Young; Rho, Hee Sool; Kim, Soonok; Kim, Byeong Ryun; Han, Seong Sook; Kang, Seogchan; Lee, Yong Hwan.

In: Molecular Microbiology, Vol. 66, No. 2, 01.10.2007, p. 371-382.

Research output: Contribution to journalArticle

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T1 - Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae

AU - Choi, Jaehyuk

AU - Park, Jongsun

AU - Jeon, Junhyun

AU - Chi, Myoung Hwan

AU - Goh, Jaeduk

AU - Yoo, Sung Yong

AU - Park, Jaejin

AU - Jung, Kyongyong

AU - Kim, Hyojeong

AU - Park, Sook Young

AU - Rho, Hee Sool

AU - Kim, Soonok

AU - Kim, Byeong Ryun

AU - Han, Seong Sook

AU - Kang, Seogchan

AU - Lee, Yong Hwan

PY - 2007/10/1

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