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 and annotation 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. 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. 2,764 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 of important plant diseases and identify biologically relevant missed genes. This study presents the first use of spectral data to edit and manually annotate an oomycete pathogen.

中文翻译：

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使用Pietophthora cinnamomi（Dieback的病原体）的蛋白质组学进行基因验证和重塑。

肉桂疫霉是致病的卵菌，在全球范围内的自然生态系统和许多重要农业作物中引起植物致死病。带注释的基因组序列草图和注释是可公开获得的（JGI Mycocosm），建议使用26,131个基因模型。在这项研究中，通过校正基因注释并发现新基因，利用肉桂假单胞菌的可溶性菌丝体，细胞外（分泌组）和游动孢子蛋白来完善基因组。通过将各种不同的子蛋白质组应用到生成的蛋白质组学流水线中，我们能够改善肉桂假单胞菌基因组。液相色谱质谱法用于获得高可信度肽段，其谱图与注释的基因组和生成的6框翻译均匹配。2，通过光谱匹配确认了来自基因组草图的764条注释。使用蛋白质组学流水线，质谱用于编辑肉桂假单胞菌基因组，并使用质谱获得的高置信度肽段鉴定23种新基因模型和60种编辑的基因特征，表明错误注释的比例为可检测到的3％蛋白质组。总体肽支持以及功能分析（包括使用基因本体论和功能域鉴定）进一步验证了这些新颖功能。我们证明了将光谱数据与我们的蛋白质组学流水线结合使用可用于改善重要植物病害的基因组并鉴定生物学相关的遗漏基因。这项研究提出了光谱数据的首次使用来编辑和手动注释卵菌病原体。