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

    OcculterCut: A comprehensive survey of AT-rich regions in fungal genomes.

    241239_241239.pdf (3.444Mb)
    Access Status
    Open access
    Authors
    Renwick, Alison
    Oliver, Richard
    Hane, James
    Date
    2016
    Type
    Journal Article
    
    Metadata
    Show full item record
    Citation
    Renwick, A. and Oliver, R. and Hane, J. 2016. OcculterCut: A comprehensive survey of AT-rich regions in fungal genomes. Genome Biology and Evolution. 8 (6): pp. 2044-2064.
    Source Title
    Genome Biology and Evolution
    DOI
    10.1093/gbe/evw121
    School
    Department of Environment and Agriculture
    URI
    http://hdl.handle.net/20.500.11937/5842
    Collection
    • Curtin Research Publications
    Abstract

    We present a novel method to measure the local GC-content bias in genomes and a survey of published fungal species. The method, enacted as "OcculterCut" (https://sourceforge.net/projects/occultercut), identified species containing distinct AT-rich regions. In most fungal taxa, AT-rich regions are a signature of repeat-induced point mutation (RIP), which targets repetitive DNA and decreases GC-content though the conversion of cytosine to thymine bases. RIP has in turn been identified as a driver of fungal genome evolution, as RIP mutations can also occur in single-copy genes neighbouring repeat-rich regions. Over time RIP perpetuates 'two speeds' of gene evolution in the GC-equilibrated and AT-rich regions of fungal genomes. In this study, genomes showing evidence of this process are found to be common, particularly among the Pezizomycotina. Further analysis highlighted differences in amino acid composition and putative functions of genes from these regions, supporting the hypothesis that these regions play an important role in fungal evolution. OcculterCut can also be used to identify genes undergoing RIP-assisted diversifying selection, such as small, secreted effector proteins that mediate host-microbe disease interactions.

    Related items

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

    • Genomic and genetic insights into a cosmopolitan fungus, paecilomyces variotii (Eurotiales)
      Urquhart, A.; Mondo, S.; Mäkelä, M.; Hane, James; Wiebenga, A.; He, G.; Mihaltcheva, S.; Pangilinan, J.; Lipzen, A.; Barry, K.; De Vries, R.; Grigoriev, I.; Idnurm, A. (2018)
      Species in the genus Paecilomyces, a member of the fungal order Eurotiales, are ubiquitous in nature and impact a variety of human endeavors. Here, the biology of one common species, Paecilomyces variotii, was explored ...
    • Effector gene prediction from fungal pathogen genome assemblies
      Testa, Alison Clare (2016)
      Fungal phytopathogens interact with their hosts largely via the secretion of effectors, which manipulate and elicit plant defences. This research contributes to the discovery of effectors from fungal pathogen genome ...
    • Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations
      Rouxel, Thierry; Graubert, Jonathan; Hane, James K.; Hoede, Claire; Van de Wouw, Angela P.; Couloux, Arnaud; Dominguez, Victoria; Anthouard, Véronique; Bally, Pascal; Bourras, Salim; Cozijnsen, Anton J.; Ciuffetti, Lynda M.; Degrave, Alexandre; Dilmaghani, Azita; Duret, Laurent; Fudal, Isabelle; Goodwin, Stephen B.; Gout, Lilian; Glaser, Nicolas; Linglin, Juliette; Kema, Gert H. J.; Lapalu, Nicolas; Lawrence, Christopher B.; May, Kim; Meyer, Michel; Ollivier, Bénédicte; Poulain, Julie; Schoch, Conrad L.; Simon, Adeline; Spatafora, Joseph W.; Stachowiak, Anna; Turgeon, B. Gillian; Tyler, Brett M.; Vincent, Delphine; Weissenbach, Jean; Amselem, Joëlle; Quesneville, Hadi; Oliver, Richard P.; Wincker, Patrick; Balesdent, Marie-Hélène; Howlett, Barbara J. (2011)
      Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi ...
    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.