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    Comprehensive annotation of the Parastagonospora nodorum reference genome using next-generation genomics, transcriptomics and proteogenomics

    245608_245608.PDF (1.905Mb)
    Access Status
    Open access
    Authors
    Syme, Robert
    Tan, Kar-Chun
    Hane, James
    Dodhia, Kejal
    Stoll, T.
    Hastie, M.
    Furuki, Eiko
    Ellwood, Simon
    Williams, A.
    Tan, Y.
    Renwick, Alison
    Gorman, J.
    Oliver, Richard
    Date
    2016
    Type
    Journal Article
    
    Metadata
    Show full item record
    Citation
    Syme, R. and Tan, K. and Hane, J. and Dodhia, K. and Stoll, T. and Hastie, M. and Furuki, E. et al. 2016. Comprehensive annotation of the Parastagonospora nodorum reference genome using next-generation genomics, transcriptomics and proteogenomics. PLoS One. 11 (2): e0147221.
    Source Title
    PLoS One
    DOI
    10.1371/journal.pone.0147221
    ISSN
    1932-6203
    School
    Department of Environment and Agriculture
    Remarks

    This open access article is distributed under the Creative Commons license http://creativecommons.org/licenses/by/4.0/

    URI
    http://hdl.handle.net/20.500.11937/7114
    Collection
    • Curtin Research Publications
    Abstract

    Parastagonospora nodorum, the causal agent of Septoria nodorum blotch (SNB), is an economically important pathogen of wheat (Triticum spp.), and a model for the study of necrotrophic pathology and genome evolution. The reference P. nodorum strain SN15 was the first Dothideomycete with a published genome sequence, and has been used as the basis for comparison within and between species. Here we present an updated reference genome assembly with corrections of SNP and indel errors in the underlying genome assembly from deep resequencing data as well as extensive manual annotation of gene models using transcriptomic and proteomic sources of evidence (https://github.com/robsyme/Parastagonospora_nodorum_SN15). The updated assembly and annotation includes 8,366 genes with modified protein sequence and 866 new genes. This study shows the benefits of using a wide variety of experimental methods allied to expert curation to generate a reliable set of gene models.

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    • Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics
      Syme, R.; Tan, K.; Hane, James; Dodhia, K.; Stoll, T.; Hastie, M.; Furuki, E.; Ellwood, Simon; Williams, A.; Tan, Y.; Testa, A.; Gorman, J.; Oliver, R. (2016)
      Parastagonospora nodorum, the causal agent of Septoria nodorum blotch (SNB), is an economically important pathogen of wheat (Triticum spp.), and a model for the study of necrotrophic pathology and genome evolution. The ...
    • Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome
      Bertazzoni, Stefania; Jones, Darcy; Phan, Huyen; Tan, Kar-Chun ; Hane, James (2021)
      Background: The fungus Parastagonospora nodorum causes septoria nodorum blotch (SNB) of wheat (Triticum aestivum) and is a model species for necrotrophic plant pathogens. The genome assembly of reference isolate Sn15 was ...
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      Bringans, S.; Hane, J.; Casey, T.; Tan, Kar-Chun; Lipscombe, R.; Solomon, P.; Oliver, Richard (2009)
      Background: Stagonospora nodorum, a fungal ascomycete in the class dothideomycetes, is a damaging pathogen of wheat. It is a model for necrotrophic fungi that cause necrotic symptoms via the interaction of multiple effector ...
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