Abstract
Repeat-induced point mutation (RIP) occurs in some fungal taxa, preferentially mutating C:G nucleotide pairs that reside within repetitive DNA and converting them to T:A. Within the taxon Pezizomycotina, RIP is biased towards mutation of CpA dinucleotides. RIP is an important feature of fungal genomes as its distribution and extent have important implications for genome evolution. Early studies of RIP did not have access to vast amounts of genome sequence information; therefore RIP was measured within one or a handful of repeat sequences using ratios of dinucleotide frequencies. However as whole-genome sequences became available for fungi, it became possible to predict the repeat content of a whole genome and calculate RIP mutation across a large number of sequences from multiple repeat families. The software tool RIPCAL was developed for this purpose and since its release has become widely used in fungal genome analysis pipelines.
Keywords
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Altschul SF, Gish W et al (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410
Amyotte SG, Tan X et al (2012) Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification. BMC Genomics 13:314
Clutterbuck AJ (2011) Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes. Fungal Genet Biol 48(3):306–326
Daverdin G, Rouxel T et al (2012) Genome structure and reproductive behaviour influence the evolutionary potential of a fungal phytopathogen. PLoS Pathog 8(11):e1003020
DiGuistini S, Wang Y et al (2011) Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. Proc Natl Acad Sci USA 108(6):2504–2509
Ellwood SR, Syme RA et al (2012) Evolution of three Pyrenophora cereal pathogens: recent divergence, speciation and evolution of non-coding DNA. Fungal Genet Biol 49(10):825–829
Fudal I, Ross S et al (2009) Repeat-induced point mutation (RIP) as an alternative mechanism of evolution toward virulence in Leptosphaeria maculans. Mol Plant Microbe Interact 22(8):932–941
Galagan JE, Selker EU (2004) RIP: the evolutionary cost of genome defense. Trends Genet 20(9):417–423
Gan P, Ikeda K et al (2013) Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi. New Phytol 197(4):1236–1249
Gao Q, Jin K et al (2011) Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum. PLoS Genet 7(1):e1001264
Hane JK, Oliver RP (2008) RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences. BMC Bioinformatics 9:478
Hane JK, Oliver RP (2010) In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes. BMC Genomics 11:655
Hood ME, Katawczik M et al (2005) Repeat-induced point mutation and the population structure of transposable elements in Microbotryum violaceum. Genetics 170(3):1081–1089
Horns F, Petit E et al (2012) Patterns of repeat-induced point mutation in transposable elements of basidiomycete fungi. Genome Biol Evol 4(3):240–247
Islam MS, Haque MS et al (2012) Tools to kill: genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina. BMC Genomics 13:493
Klosterman SJ, Subbarao KV et al (2011) Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathog 7(7):e1002137
Larkin MA, Blackshields G et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948
Lefebvre F, Joly DL et al (2013) The transition from a phytopathogenic smut ancestor to an anamorphic biocontrol agent deciphered by comparative whole-genome analysis. Plant Cell 25(6):1946–1959
Lord PW, Selley JN et al (2002) CINEMA-MX: a modular multiple alignment editor. Bioinformatics 18(10):1402–1403
Manning VA, Pandelova I et al (2013) Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3 3(1):41–63
Margolin BS, Garrett-Engele PW et al (1998) A methylated Neurospora 5S rRNA pseudogene contains a transposable element inactivated by repeat-induced point mutation. Genetics 149(4):1787–1797
Price AL, Jones NC et al (2005) De novo identification of repeat families in large genomes. Bioinformatics 21(Suppl 1):i351–i358
Ropars J, Dupont J et al (2012) Sex in cheese: evidence for sexuality in the fungus Penicillium roqueforti. PLoS One 7(11):e49665
Rouxel T, Grandaubert J et al (2011) Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nat Commun 2:202
Santana MF, Silva JC et al (2012) Abundance, distribution and potential impact of transposable elements in the genome of Mycosphaerella fijiensis. BMC Genomics 13:720
Selker EU, Stevens JN (1987) Signal for DNA methylation associated with tandem duplication in Neurospora crassa. Mol Cell Biol 7(3):1032–1038
Selker EU, Cambareri EB et al (1987) Rearrangement of duplicated DNA in specialized cells of Neurospora. Cell 51(5):741–752
Smit AFA, Hubley R et al (1996–2010) RepeatMasker Open-3.0. http://www.repeatmasker.org
Van de Wouw AP, Cozijnsen AJ et al (2010) Evolution of linked avirulence effectors in Leptosphaeria maculans is affected by genomic environment and exposure to resistance genes in host plants. PLoS Pathog 6(11):e1001180
Vogel KJ, Moran NA (2013) Functional and evolutionary analysis of the genome of an obligate fungal symbiont. Genome Biol Evol 5(5):891–904
Walsh CP, Xu GL (2006) Cytosine methylation and DNA repair. Curr Top Microbiol Immunol 301:283–315
Waterhouse AM, Procter JB et al (2009) Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25(9):1189–1191
Yang J, Wang L et al (2011) Genomic and proteomic analyses of the fungus Arthrobotrys oligospora provide insights into nematode-trap formation. PLoS Pathog 7(9):e1002179
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Hane, J.K. (2015). Calculating RIP Mutation in Fungal Genomes Using RIPCAL. In: van den Berg, M., Maruthachalam, K. (eds) Genetic Transformation Systems in Fungi, Volume 2. Fungal Biology. Springer, Cham. https://doi.org/10.1007/978-3-319-10503-1_5
Download citation
DOI: https://doi.org/10.1007/978-3-319-10503-1_5
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-10502-4
Online ISBN: 978-3-319-10503-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)