ArticleBMC genomics2010
In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Characterization and organization of telomeric-linked helicase (tlh) gene families in Fusarium oxysporum.Current genetics · 2024Article
- Update on the Basic Understanding ofPlants (Basel, Switzerland) · 2024Review
- Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen.PLoS pathogens · 2023Article
- Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen.Microbial genomics · 2021Article
- Article
- Genome-Wide Analyses of Repeat-Induced Point Mutations in the Ascomycota.Frontiers in microbiology · 2020Article
- Variable genome evolution in fungi after transposon-mediated amplification of a housekeeping gene.Mobile DNA · 2019Article
- The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations.PeerJ · 2019Article
- Pan-Parastagonospora Comparative Genome Analysis-Effector Prediction and Genome Evolution.Genome biology and evolution · 2018Article
- Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity.BMC genomics · 2018Article
- Transposable Element Genomic Fissuring inFrontiers in genetics · 2018Article
- Article
- OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes.Genome biology and evolution · 2016Article
- Draft genome sequencing and secretome analysis of fungal phytopathogen Ascochyta rabiei provides insight into the necrotrophic effector repertoire.Scientific reports · 2016Article
- Article
- Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens.BMC genomics · 2014Article
- The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species.BMC genomics · 2014Article
- Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8.PLoS genetics · 2014Article
- Resequencing and comparative genomics of Stagonospora nodorum: sectional gene absence and effector discovery.G3 (Bethesda, Md.) · 2013Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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