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 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 stu...
| Main Authors: | , , , , , , |
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| Format: | Journal Article |
| Published: |
Frontiers Media
2021
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| Online Access: | http://hdl.handle.net/20.500.11937/83831 |
| _version_ | 1848764607819153408 |
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| author | Andronis, Christina Hane, James Bringans, Scott Hardy, Giles Jacques, Silke Lipscombe, Richard Tan, Kar-Chun |
| author_facet | Andronis, Christina Hane, James Bringans, Scott Hardy, Giles Jacques, Silke Lipscombe, Richard Tan, Kar-Chun |
| author_sort | Andronis, Christina |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-14T11:22:03Z |
| format | Journal Article |
| id | curtin-20.500.11937-83831 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T11:22:03Z |
| publishDate | 2021 |
| publisher | Frontiers Media |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-838312021-08-15T23:51:03Z Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of Dieback Andronis, Christina Hane, James Bringans, Scott Hardy, Giles Jacques, Silke Lipscombe, Richard Tan, Kar-Chun 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. 2021 Journal Article http://hdl.handle.net/20.500.11937/83831 10.21203/rs.3.rs-96087/v1 http://creativecommons.org/licenses/by/4.0/ Frontiers Media fulltext |
| spellingShingle | Andronis, Christina Hane, James Bringans, Scott Hardy, Giles Jacques, Silke Lipscombe, Richard Tan, Kar-Chun Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of Dieback |
| title | Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of Dieback |
| title_full | Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of Dieback |
| title_fullStr | Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of Dieback |
| title_full_unstemmed | Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of Dieback |
| title_short | Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of Dieback |
| title_sort | gene validation and remodelling using proteogenomics of phytophthora cinnamomi, the causal agent of dieback |
| url | http://hdl.handle.net/20.500.11937/83831 |