Cargando…

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 study,...

Descripción completa

Detalles Bibliográficos
Autores principales: Andronis, Christina E., Hane, James K., Bringans, Scott, Hardy, Giles E. S. J., Jacques, Silke, Lipscombe, Richard, Tan, Kar-Chun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8360494/
https://www.ncbi.nlm.nih.gov/pubmed/34394023
http://dx.doi.org/10.3389/fmicb.2021.665396
_version_ 1783737753898319872
author Andronis, Christina E.
Hane, James K.
Bringans, Scott
Hardy, Giles E. S. J.
Jacques, Silke
Lipscombe, Richard
Tan, Kar-Chun
author_facet Andronis, Christina E.
Hane, James K.
Bringans, Scott
Hardy, Giles E. S. J.
Jacques, Silke
Lipscombe, Richard
Tan, Kar-Chun
author_sort Andronis, Christina E.
collection PubMed
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.
format Online
Article
Text
id pubmed-8360494
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-83604942021-08-13 Gene Validation and Remodelling Using Proteogenomics of Phytophthora cinnamomi, the Causal Agent of Dieback Andronis, Christina E. Hane, James K. Bringans, Scott Hardy, Giles E. S. J. Jacques, Silke Lipscombe, Richard Tan, Kar-Chun Front Microbiol Microbiology 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. Frontiers Media S.A. 2021-07-15 /pmc/articles/PMC8360494/ /pubmed/34394023 http://dx.doi.org/10.3389/fmicb.2021.665396 Text en Copyright © 2021 Andronis, Hane, Bringans, Hardy, Jacques, Lipscombe and Tan. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Andronis, Christina E.
Hane, James K.
Bringans, Scott
Hardy, Giles E. S. J.
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
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8360494/
https://www.ncbi.nlm.nih.gov/pubmed/34394023
http://dx.doi.org/10.3389/fmicb.2021.665396
work_keys_str_mv AT andronischristinae genevalidationandremodellingusingproteogenomicsofphytophthoracinnamomithecausalagentofdieback
AT hanejamesk genevalidationandremodellingusingproteogenomicsofphytophthoracinnamomithecausalagentofdieback
AT bringansscott genevalidationandremodellingusingproteogenomicsofphytophthoracinnamomithecausalagentofdieback
AT hardygilesesj genevalidationandremodellingusingproteogenomicsofphytophthoracinnamomithecausalagentofdieback
AT jacquessilke genevalidationandremodellingusingproteogenomicsofphytophthoracinnamomithecausalagentofdieback
AT lipscomberichard genevalidationandremodellingusingproteogenomicsofphytophthoracinnamomithecausalagentofdieback
AT tankarchun genevalidationandremodellingusingproteogenomicsofphytophthoracinnamomithecausalagentofdieback