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Open Access Research article

In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes

James K Hane13 and Richard P Oliver2*

Author Affiliations

1 Faculty of Health Sciences, Murdoch University, Perth, Western Australia, 6150, Australia

2 Department of Environment and Agriculture, Curtin University, Perth, Western Australia, 6102, Australia

3 Current address: CSIRO Plant Industry, CELS Floreat, Perth, Western Australia, 6014, Australia

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BMC Genomics 2010, 11:655  doi:10.1186/1471-2164-11-655

Published: 24 November 2010

Abstract

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 nodorum SN15 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. DeRIP is open-source and is available as part of the RIPCAL suite at http://www.sourceforge.net/projects/ripcal webcite.