Journal article
Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum
BMC Bioinformatics, Vol.10(1)
2009
Abstract
Background
Stagonospora nodorum, a fungal ascomycete in the class dothideomycetes, is a damaging pathogen of wheat. It is a model for necrotrophic fungi that cause necrotic symptoms via the interaction of multiple effector proteins with cultivar-specific receptors. A draft genome sequence and annotation was published in 2007. A second-pass gene prediction using a training set of 795 fully EST-supported genes predicted a total of 10762 version 2 nuclear-encoded genes, with an additional 5354 less reliable version 1 genes also retained.
Results
In this study, we subjected soluble mycelial proteins to proteolysis followed by 2D LC MALDI-MS/MS. Comparison of the detected peptides with the gene models validated 2134 genes. 62% of these genes (1324) were not supported by prior EST evidence. Of the 2134 validated genes, all but 188 were version 2 annotations. Statistical analysis of the validated gene models revealed a preponderance of cytoplasmic and nuclear localised proteins, and proteins with intracellular-associated GO terms. These statistical associations are consistent with the source of the peptides used in the study. Comparison with a 6-frame translation of the S. nodorum genome assembly confirmed 905 existing gene annotations (including 119 not previously confirmed) and provided evidence supporting 144 genes with coding exon frameshift modifications, 604 genes with extensions of coding exons into annotated introns or untranslated regions (UTRs), 3 new gene annotations which were supported by tblastn to NR, and 44 potential new genes residing within un-assembled regions of the genome.
Conclusion
We conclude that 2D LC MALDI-MS/MS is a powerful, rapid and economical tool to aid in the annotation of fungal genomic assemblies.
Details
- Title
- Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum
- Authors/Creators
- S. Bringans (Author/Creator) - Proteomics International, Perth, AustraliaJ.K. Hane (Author/Creator) - Murdoch UniversityT. Casey (Author/Creator) - Proteomics International, Perth, AustraliaK-C Tan (Author/Creator) - Murdoch UniversityR. Lipscombe (Author/Creator) - Proteomics International, Perth, AustraliaP.S. Solomon (Author/Creator) - Australian National UniversityR.P. Oliver (Author/Creator) - Murdoch University
- Publication Details
- BMC Bioinformatics, Vol.10(1)
- Publisher
- BioMed Central
- Identifiers
- 991005542189007891
- Copyright
- © 2009 Bringans et al
- Murdoch Affiliation
- Australian Centre for Necrotrophic Fungal Pathogens; School of Veterinary and Biomedical Sciences
- Language
- English
- Resource Type
- Journal article
- Note
- This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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- Collaboration types
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- Citation topics
- 2 Chemistry
- 2.211 Mass Spectrometry
- 2.211.497 Proteomics Mass Spectrometry
- Web Of Science research areas
- Biochemical Research Methods
- Biotechnology & Applied Microbiology
- Mathematical & Computational Biology
- ESI research areas
- Computer Science