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    Comparative genomics and prediction of conditionally dispensable sequences in legume–infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors

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    Access Status
    Open access
    Authors
    Williams, A.
    Sharma, M.
    Thatcher, L.
    Azam, S.
    Hane, James
    Sperschneider, J.
    Kidd, B.
    Anderson, J.
    Ghosh, R.
    Garg, G.
    Lichtenzveig, J.
    Kistler, H.
    Shea, T.
    Young, S.
    Buck, S.
    Kamphuis, L.
    Saxena, R.
    Pande, S.
    Ma, L.
    Varshney, R.
    Singh, K.
    Date
    2016
    Type
    Journal Article
    
    Metadata
    Show full item record
    Citation
    Williams, A. and Sharma, M. and Thatcher, L. and Azam, S. and Hane, J. and Sperschneider, J. and Kidd, B. et al. 2016. Comparative genomics and prediction of conditionally dispensable sequences in legume–infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors. BMC Genomics. 17: 191.
    Source Title
    BMC Genomics
    DOI
    10.1186/s12864-016-2486-8
    School
    Centre for Crop Disease Management
    Remarks

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

    URI
    http://hdl.handle.net/20.500.11937/47903
    Collection
    • Curtin Research Publications
    Abstract

    Background: Soil-borne fungi of the Fusarium oxysporum species complex cause devastating wilt disease on many crops including legumes that supply human dietary protein needs across many parts of the globe. We present and compare draft genome assemblies for three legume-infecting formae speciales (ff. spp.): F. oxysporum f. sp. ciceris (Foc-38-1) and f. sp. pisi (Fop-37622), significant pathogens of chickpea and pea respectively, the world’s second and third most important grain legumes, and lastly f. sp. medicaginis (Fom-5190a) for which we developed a model legume pathosystem utilising Medicago truncatula. Results: Focusing on the identification of pathogenicity gene content, we leveraged the reference genomes of Fusarium pathogens F. oxysporum f. sp. lycopersici (tomato-infecting) and F. solani (pea-infecting) and their well-characterised core and dispensable chromosomes to predict genomic organisation in the newly sequenced legume-infecting isolates. Dispensable chromosomes are not essential for growth and in Fusarium species are known to be enriched in host-specificity and pathogenicity-associated genes. Comparative genomics of the publicly available Fusarium species revealed differential patterns of sequence conservation across F. oxysporum formae speciales, with legume-pathogenic formae speciales not exhibiting greater sequence conservation between them relative to non-legume-infecting formae speciales, possibly indicating the lack of a common ancestral source for legume pathogenicity. Combining predicted dispensable gene content with in planta expression in the model legume-infecting isolate, we identified small conserved regions and candidate effectors, four of which shared greatest similarity to proteins from another legume-infecting ff. spp. Conclusions: We demonstrate that distinction of core and potential dispensable genomic regions of novel F. oxysporum genomes is an effective tool to facilitate effector discovery and the identification of gene content possibly linked to host specificity. While the legume-infecting isolates didn’t share large genomic regions of pathogenicity-related content, smaller regions and candidate effector proteins were highly conserved, suggesting that they may play specific roles in inducing disease on legume hosts.

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