55 M.A. van den Berg and K. Maruthachalam (eds.), Genetic Transformation Systems in Fungi, Volume 2, Fungal Biology, DOI 10.1007/978-3-319-10503-1_4, © Springer International Publishing Switzerland 2015 4.1 Introduction 4.1.1 Observations of RIP in Neurospora crassa RIP was first identified in Neurospora crassa by Selker and colleagues (Selker et al. 1987a) and subsequently identified in a number of fungal spe- cies. The main outcome of RIP is to induce transi- tion mutations (interchanges between pyrimidines or between purine bases, i.e., C↔T or G↔A) in repeated sequences during the sexual stage of the fungal life-cycle. The effects of RIP were first iden- tified in the progeny of a cross of N. crassa isolates carrying a transformation vector designed to inves- tigate DNA methylation control in Neurospora (Selker et al. 1987b). This study found that the introduced DNA sequences that were homologous to those in the host genome were rapidly mutated in ascogenous hyphae, with both copies of the duplicated sequences displaying the mutations. The phenomenon of RIP was noted to occur after fertilization but before meiosis, during a brief pre- meiotic phase in which a dikaryon is formed prior to nuclear duplication and karyogamy (nuclear fusion) (Selker et al. 1987a; Selker 1990). For this reason, the acronym “RIP” for “rearrange- ment induced premeiotically” was initially used to describe the process but was retroactively changed to “repeat-induced point (mutation)”. These early studies of RIP identified numer- ous transition mutations from C:G to T:A base pairs within the regions of repetitive DNA (Selker et al. 1987a; Selker 1990). Furthermore, the fre- quency of cytosine transitions was found to be strongly biased towards cytosine bases adjacent to a downstream adenine base (CpA) (Cambareri et al. 1989). The CpA dinucleotide is thus changed to TpA, while the TpG sequence on the opposite strand is also converted to TpA. This dinucleotide mutation bias has since been widely observed across the Pezizomycotina (filamentous Ascomycota) (Clutterbuck 2011). In N. crassa RIP was observed to operate in successive sexual cycles until the sequence iden- tity between pairs of repeated sequences was reduced below the minimum similarity threshold of ~80 % (Cambareri et al. 1989). Repetitive sequences were observed to be mutated by RIP for up to six generations (Cambareri et al. 1991), until they became too dissimilar. In a single J.K. Hane, BMolBiol. (Hons.), Ph. D. Bioinformatics (*) R.P. Oliver, B.Sc., Ph.D. Biochem. Centre for Crop and Disease Management, Curtin University, Perth, WA, Australia e-mail: James.Hane@curtin.edu.au A.H. Williams, B. Appl. Sci. (Hons.) The Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia A.P. Taranto, B.Sc. (Hons.) • P.S. Solomon, B. Appl. Sci. (Hons.), Ph.D. Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, Australia 4 Repeat-Induced Point Mutation: A Fungal-Specific, Endogenous Mutagenesis Process James K. Hane, Angela H. Williams, Adam P. Taranto, Peter S. Solomon, and Richard P. Oliver