| Summary: | 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.
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