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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...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Blackwell Publishing Ltd
2007
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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. |
format | Text |
id | pubmed-2169514 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | Blackwell Publishing Ltd |
record_format | MEDLINE/PubMed |
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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