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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 repo...

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Autores principales: 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
Formato: Texto
Lenguaje:English
Publicado: Blackwell Publishing Ltd 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2169514/
https://www.ncbi.nlm.nih.gov/pubmed/17850257
http://dx.doi.org/10.1111/j.1365-2958.2007.05918.x
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author 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
author_facet 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
author_sort Choi, Jaehyuk
collection PubMed
description 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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spelling pubmed-21695142008-01-09 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 Mol Microbiol Research Articles 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. Blackwell Publishing Ltd 2007-10 /pmc/articles/PMC2169514/ /pubmed/17850257 http://dx.doi.org/10.1111/j.1365-2958.2007.05918.x Text en © 2007 The Authors; Journal compilation © 2007 Blackwell Publishing Ltd https://creativecommons.org/licenses/by/2.5/ Present address: Department of Plant Pathology, Pennsylvania State University, University Park, PA 16802, USA.Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation.
spellingShingle Research Articles
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
title Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae
title_full Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae
title_fullStr Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae
title_full_unstemmed Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae
title_short Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae
title_sort genome-wide analysis of t-dna integration into the chromosomes of magnaporthe oryzae
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2169514/
https://www.ncbi.nlm.nih.gov/pubmed/17850257
http://dx.doi.org/10.1111/j.1365-2958.2007.05918.x
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