Curtin University Homepage
  • Library
  • Help
    • Admin

    espace - Curtin’s institutional repository

    JavaScript is disabled for your browser. Some features of this site may not work without it.
    View Item 
    • espace Home
    • espace
    • Curtin Research Publications
    • View Item
    • espace Home
    • espace
    • Curtin Research Publications
    • View Item

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

    Access Status
    Fulltext not available
    Authors
    Hane, J.
    Oliver, Richard
    Date
    2008
    Type
    Journal Article
    
    Metadata
    Show full item record
    Citation
    HANE JK & OLIVER RP (2008) RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences. BMC Bioinformatics 9 art. No 478
    DOI
    10.1186/1471-2105-9-478
    Faculty
    Department of Environmental & Agriculture
    School of Agriculture and Environment
    Faculty of Science and Engineering
    Remarks

    A copy of this item may be available from Professor Richard Oliver

    Email: Richard.oliver@curtin.edu.au

    URI
    http://hdl.handle.net/20.500.11937/46040
    Collection
    • Curtin Research Publications
    Abstract

    Background: 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. Result: We present RIPCAL http://www.sourceforge.net/projects/ripcal webcite, 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. Conclusion: 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.

    Related items

    Showing items related by title, author, creator and subject.

    • Repeat-Induced Point Mutation in Fungi: A Fungal-Specific Endogenous Mutagenesis Process
      Hane, James; Williams, A.; Taranto, A.; Solomon, P.; Oliver, Richard (2015)
      Repeat-induced point mutation (RIP) is a form of genome mutation that is targeted towards repeated DNA sequences and which is observed only in certain fungal taxa; the Pezizomycotina (filamentous Ascomycota) and some ...
    • A genome-wide genetic linkage map and reference quality genome sequence for a new race in the wheat pathogen Pyrenophora tritici-repentis
      Kariyawasam, G.K.; Wyatt, N.; Shi, G.; Liu, S.; Yan, C.; Ma, Y.; Zhong, S.; Rasmussen, J.B.; Moolhuijzen, Paula ; Moffat, Caroline ; Friesen, T.L.; Liu, Z. (2021)
      Pyrenophora tritici-repentis is an ascomycete fungus that causes tan spot of wheat. The disease has a worldwide distribution and can cause significant yield and quality losses in wheat production. The fungal pathogen is ...
    • The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species.
      Pattemore, J.; Hane, James; Williams, Angela; Wilson, B.; Stodart, B.; Ash, G. (2014)
      Background: Metarhizium anisopliae is an important fungal biocontrol agent of insect pests of agricultural crops. Genomics can aid the successful commercialization of biopesticides by identification of key genes differentiating ...
    Advanced search

    Browse

    Communities & CollectionsIssue DateAuthorTitleSubjectDocument TypeThis CollectionIssue DateAuthorTitleSubjectDocument Type

    My Account

    Admin

    Statistics

    Most Popular ItemsStatistics by CountryMost Popular Authors

    Follow Curtin

    • 
    • 
    • 
    • 
    • 

    CRICOS Provider Code: 00301JABN: 99 143 842 569TEQSA: PRV12158

    Copyright | Disclaimer | Privacy statement | Accessibility

    Curtin would like to pay respect to the Aboriginal and Torres Strait Islander members of our community by acknowledging the traditional owners of the land on which the Perth campus is located, the Whadjuk people of the Nyungar Nation; and on our Kalgoorlie campus, the Wongutha people of the North-Eastern Goldfields.