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

BMC Genomics

Research Article

Richard P Oliver¹  James K Hane² 

[1] Department of Environment and Agriculture, Curtin University, 6102, Perth, Western Australia, Australia;Faculty of Health Sciences, Murdoch University, 6150, Perth, Western Australia, Australia;CSIRO Plant Industry, CELS Floreat, 6014, Perth, Western Australia, Australia;

关键词: Repeat Family;    rDNA Repeat;    Australian Isolate;    Active Copy;    Majority Consensus;   

DOI  :  10.1186/1471-2164-11-655

 received in 2010-08-12, accepted in 2010-11-24,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundRepeat-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.ResultsDeRIP 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.ConclusionsFive 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.

【 授权许可】

CC BY   
© Hane and Oliver; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.