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dc.contributor.authorAndronis, Christina
dc.contributor.authorHane, James
dc.contributor.authorBringans, Scott
dc.contributor.authorHardy, Giles
dc.contributor.authorJacques, Silke
dc.contributor.authorLipscombe, Richard
dc.contributor.authorTan, Kar-Chun
dc.identifier.citationAndronis, C. and Hane, J. and Bringans, S. and Hardy, G. and Jacques, S. and Lipscombe, R. and Tan, K.-C. 2021. Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of Dieback. Frontiers in Microbiology. 12: Article No. 665396.

Phytophthora cinnamomi is a pathogenic oomycete that causes plant dieback disease across a range of natural ecosystems and in many agriculturally important crops on a global scale. An annotated draft genome sequence is publicly available (JGI Mycocosm) and suggests 26,131 gene models. In this study, soluble mycelial, extracellular (secretome), and zoospore proteins of P. cinnamomi were exploited to refine the genome by correcting gene annotations and discovering novel genes. By implementing the diverse set of sub-proteomes into a generated proteogenomics pipeline, we were able to improve the P. cinnamomi genome annotation. Liquid chromatography mass spectrometry was used to obtain high confidence peptides with spectral matching to both the annotated genome and a generated 6-frame translation. Two thousand seven hundred sixty-four annotations from the draft genome were confirmed by spectral matching. Using a proteogenomic pipeline, mass spectra were used to edit the P. cinnamomi genome and allowed identification of 23 new gene models and 60 edited gene features using high confidence peptides obtained by mass spectrometry, suggesting a rate of incorrect annotations of 3% of the detectable proteome. The novel features were further validated by total peptide support, alongside functional analysis including the use of Gene Ontology and functional domain identification. We demonstrated the use of spectral data in combination with our proteogenomics pipeline can be used to improve the genome annotation of important plant diseases and identify missed genes. This study presents the first use of spectral data to edit and manually annotate an oomycete pathogen.

dc.publisherFrontiers Media
dc.titleGene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of Dieback
dc.typeJournal Article
dcterms.source.titleFrontiers in Microbiology
curtin.departmentSchool of Molecular and Life Sciences (MLS)
curtin.accessStatusOpen access
curtin.facultyFaculty of Science and Engineering
curtin.contributor.orcidTan, Kar-Chun [0000-0001-6094-823X]
curtin.contributor.scopusauthoridTan, Kar-Chun [56231324800] [7403999337]

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