Gene Validation and Remodelling Using Proteogenomics of Phytophthora cinnamomi, the Causal Agent of Dieback

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