In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes.
Background: Repeat-induced point mutation (RIP) is a fungal genome defence mechanism guarding against transposon invasion. RIP mutates the sequence of repeated DNA and over time renders the affected regions unrecognisable by similarity search tools such as BLAST. Results: DeRIP is a new software too...
| Main Authors: | , |
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| Format: | Journal Article |
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Biomed Central
2010
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| Online Access: | http://hdl.handle.net/20.500.11937/28231 |
| _version_ | 1848752480701120512 |
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| author | Hane, J. Oliver, Richard |
| author_facet | Hane, J. Oliver, Richard |
| author_sort | Hane, J. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Background: Repeat-induced point mutation (RIP) is a fungal genome defence mechanism guarding against transposon invasion. RIP mutates the sequence of repeated DNA and over time renders the affected regions unrecognisable by similarity search tools such as BLAST. Results: DeRIP is a new software tool developed to predict the original sequence of a RIP-mutated region prior to the occurrence of RIP. In this study, we apply deRIP to the genome of the wheat pathogen Stagonospora nodorumSN15 and predict the origin of several previously uncharacterised classes of repetitive DNA. Conclusions: Five new classes of transposon repeats and four classes of endogenous gene repeats were identified after deRIP. The deRIP process is a new tool for fungal genomics that facilitates the identification and understanding of the role and origin of fungal repetitive DNA. |
| first_indexed | 2025-11-14T08:09:18Z |
| format | Journal Article |
| id | curtin-20.500.11937-28231 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T08:09:18Z |
| publishDate | 2010 |
| publisher | Biomed Central |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-282312017-09-13T15:19:35Z In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes. Hane, J. Oliver, Richard Background: Repeat-induced point mutation (RIP) is a fungal genome defence mechanism guarding against transposon invasion. RIP mutates the sequence of repeated DNA and over time renders the affected regions unrecognisable by similarity search tools such as BLAST. Results: DeRIP is a new software tool developed to predict the original sequence of a RIP-mutated region prior to the occurrence of RIP. In this study, we apply deRIP to the genome of the wheat pathogen Stagonospora nodorumSN15 and predict the origin of several previously uncharacterised classes of repetitive DNA. Conclusions: Five new classes of transposon repeats and four classes of endogenous gene repeats were identified after deRIP. The deRIP process is a new tool for fungal genomics that facilitates the identification and understanding of the role and origin of fungal repetitive DNA. 2010 Journal Article http://hdl.handle.net/20.500.11937/28231 10.1186/1471-2164-11-655 Biomed Central fulltext |
| spellingShingle | Hane, J. Oliver, Richard In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes. |
| title | In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes. |
| title_full | In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes. |
| title_fullStr | In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes. |
| title_full_unstemmed | In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes. |
| title_short | In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes. |
| title_sort | in silico reversal of repeat-induced point mutation (rip) identifies the origins of repeat families and uncovers obscured duplicated genes. |
| url | http://hdl.handle.net/20.500.11937/28231 |