Abstract
BackgroundRepeat-induced point mutation (RIP) is a fungal-specific genome defence mechanism that alters the sequences of repetitive DNA, thereby inactivating coding genes. Repeated DNA sequences align between mating and meiosis and both sequences undergo C:G to T:A transitions. In most fungi these transitions preferentially affect CpA di-nucleotides thus altering the frequency of certain di-nucleotides in the affected sequences. The majority of previously published in silico analyses were limited to the comparison of ratios of pre- and post-RIP di-nucleotides in putatively RIP-affected sequences – so-called RIP indices. The analysis of RIP is significantly more informative when comparing sequence alignments of repeated sequences. There is, however, a dearth of bioinformatics tools available to the fungal research community for alignment-based RIP analysis of repeat families.ResultsWe present RIPCAL , a software tool for the automated analysis of RIP in fungal genomic DNA repeats, which performs both RIP index and alignment-based analyses. We demonstrate the ability of RIPCAL to detect RIP within known RIP-affected sequences of Neurospora crassa and other fungi. We also predict and delineate the presence of RIP in the genome of Stagonospora nodorum – a Dothideomycete pathogen of wheat. We show that RIP has affected different members of the S. nodorum rDNA tandem repeat to different extents depending on their genomic contexts.ConclusionThe RIPCAL alignment-based method has considerable advantages over RIP indices for the analysis of whole genomes. We demonstrate its application to the recently published genome assembly of S. nodorum.
Highlights
Repeat-induced point mutation (RIP) is a fungal-specific genome defence mechanism that alters the sequences of repetitive DNA, thereby inactivating coding genes
Validation of RIP detection by the alignment-based method The RIPCAL alignment-based method was applied to both the 5S rDNA repeat family of Neurospora crassa, which is reportedly free from RIP mutation due to its short sequence length [17], and to the Tad1 transposons of N. crassa, which are reported to be heavily prone to CpA→TpA RIP mutation [23]
The MATE transposon repeat family of Aspergillus nidulans and the Ty1 Copia-like transposon family of the Basidiomycete Microbotryum violaceum were analysed by RIPCAL
Summary
Repeat-induced point mutation (RIP) is a fungal-specific genome defence mechanism that alters the sequences of repetitive DNA, thereby inactivating coding genes. Repeated DNA sequences align between mating and meiosis and both sequences undergo C:G to T:A transitions. Over 100 fungal genome sequences have been obtained or are in the pipeline [1] and next-generation sequencing technologies will further accelerate the accumulation of data over the decade. This rapidly growing array of sequence information presents many new challenges for analysis. RIP is believed to be a defence (page number not for citation purposes)
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