ArticleBMC bioinformatics2009
Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- EffectorFisher: association of disease phenotype with pangenomic protein-isoform profiles for improved prediction of fungal pathogenicity effectors.Scientific reports · 2026Article
- Repeat-induced point mutations driving Parastagonospora nodorum genomic diversity are balanced by selection against non-synonymous mutations.Communications biology · 2024Article
- Review
- Article
- Gene Validation and Remodelling Using Proteogenomics ofFrontiers in microbiology · 2021Article
- A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant-microbe interactions and legume evolution.Plant biotechnology journal · 2017Article
- Article
- Evaluation of Secretion Prediction Highlights Differing Approaches Needed for Oomycete and Fungal Effectors.Frontiers in plant science · 2015Article
- Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments.Molecular & cellular proteomics : MCP · 2013Article
- Resequencing and comparative genomics of Stagonospora nodorum: sectional gene absence and effector discovery.G3 (Bethesda, Md.) · 2013Article
- Transcriptome analysis of Stagonospora nodorum: gene models, effectors, metabolism and pantothenate dispensability.Molecular plant pathology · 2012Article
- The Rice Proteogenomics Database OryzaPG-DB: Development, Expansion, and New Features.Frontiers in plant science · 2012Article
- Pyrenophora teres: profile of an increasingly damaging barley pathogen.Molecular plant pathology · 2011Review
- A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi.Genome biology · 2011Article
- A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres.Genome biology · 2010Article
- Proteomics of plant pathogenic fungi.Journal of biomedicine & biotechnology · 2010Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundStagonospora 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.
resultsIn 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.
conclusionWe conclude that 2D LC MALDI-MS/MS is a powerful, rapid and economical tool to aid in the annotation of fungal genomic assemblies.
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