RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences

• Published in: BMC bioinformatics Vol. 9; no. 1; p. 478
• Main Authors: Hane, James K, Oliver, Richard P
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 12-11-2008; BioMed Central; BMC
• Subjects: Algorithms; Ascomycota - genetics; Computational Biology - methods; Computer programs; Dothideomycetes; Genomics - methods; Methodology; Molecular Sequence Data; Neurospora crassa; Point Mutation - genetics; Repetitive Sequences, Nucleic Acid - genetics; Science; Sequence Alignment; Software; Stagonospora nodorum; Triticum aestivum
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-9-478

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. 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.
We present RIPCAL http://www.sourceforge.net/projects/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.
The 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.