Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of dieback

C.E. Andronis; J.K. Hane; S. Bringans; G.E.S.J. Hardy; S. Jacques; R. Lipscombe; K-C Tan

doi:10.3389/fmicb.2021.665396

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Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of dieback

C.E. Andronis, J.K. Hane, S. Bringans, G.E.S.J. Hardy, S. Jacques, R. Lipscombe and K-C Tan

Frontiers in Microbiology, Vol.12, Art. 665396

2021

DOI: https://doi.org/10.3389/fmicb.2021.665396

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Abstract

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.

Details

Title: Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of dieback
Authors/Creators: C.E. Andronis (Author/Creator) - Curtin University
J.K. Hane (Author/Creator) - Curtin University
S. Bringans (Author/Creator) - Proteomics International, Nedlands, WA, Australia.
G.E.S.J. Hardy (Author/Creator) - Murdoch University
S. Jacques (Author/Creator) - Curtin University
R. Lipscombe (Author/Creator) - Proteomics International, Nedlands, WA, Australia.
K-C Tan (Author/Creator) - Curtin University
Publication Details: Frontiers in Microbiology, Vol.12, Art. 665396
Publisher: Frontiers
Identifiers: 991005543404207891
Copyright: © 2021 The Authors.
Murdoch Affiliation: Centre for Phytophthora Science and Management
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.419 Jasmonic Acid
Web Of Science research areas: Microbiology
ESI research areas: Microbiology