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Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum

Bringans, Scott; Hane, James; Casey, Tammy; Tan, Kar-Chun; Lipscombe, Richard J; Solomon, Peter S; Oliver, Richard Peter

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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...[Show more]

dc.contributor.authorBringans, Scott
dc.contributor.authorHane, James
dc.contributor.authorCasey, Tammy
dc.contributor.authorTan, Kar-Chun
dc.contributor.authorLipscombe, Richard J
dc.contributor.authorSolomon, Peter S
dc.contributor.authorOliver, Richard Peter
dc.date.accessioned2010-08-27T03:49:32Z
dc.date.accessioned2010-12-20T06:03:38Z
dc.date.available2010-08-27T03:49:32Z
dc.date.available2010-12-20T06:03:38Z
dc.identifier.citationBMC Bioinformatics 10.301 (2009)
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/10440/1072
dc.identifier.urihttp://digitalcollections.anu.edu.au/handle/10440/1072
dc.description.abstractBACKGROUND: 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 intracellularassociated 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.
dc.format9 pages
dc.publisherBioMed Central Ltd
dc.rights© 2009 Bringans et al; licensee BioMed Central Ltd. 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.
dc.sourceBMC Bioinformatics
dc.source.urihttp://www.biomedcentral.com/content/pdf/1471-2105-10-301.pdf
dc.source.urihttp://www.biomedcentral.com/1471-2105/10/301
dc.source.urihttp://dx.doi.org/
dc.subjectKeywords: Gene annotation; Gene prediction; Genome assembly; Genome sequences; High throughput; Multidimensional liquid chromatography; Necrotic symptoms; Untranslated regions; Fungi; Liquid chromatography; Mass spectrometry; Peptides; Genes; fungal protein; peptid
dc.titleDeep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum
dc.typeJournal article
local.identifier.citationvolume10
dcterms.dateAccepted2009-09-22
dc.date.issued2009-09-22
local.identifier.absfor060109
local.identifier.ariespublicationu4632004xPUB3
local.publisher.urlhttp://www.biomedcentral.com/
local.type.statusPublished Version
local.contributor.affiliationBringans, Scott, Proteomics International Pty Ltd
local.contributor.affiliationHane, James, Murdoch University
local.contributor.affiliationCasey, Tammy, Proteomics International Pty Ltd
local.contributor.affiliationTan, Kar-Chun, Murdoch University
local.contributor.affiliationLipscombe, Richard J, Proteomics International Pty Ltd
local.contributor.affiliationSolomon, Peter, College of Medicine, Biology and Environment, ANU
local.contributor.affiliationOliver, Richard Peter, Murdoch University
local.bibliographicCitation.issue301
local.bibliographicCitation.startpage9
local.identifier.doi10.1186/1471-2105-10-301
dc.date.updated2016-02-24T11:15:23Z
local.identifier.scopusID2-s2.0-70449372306
local.identifier.thomsonID000270276800001
CollectionsANU Research Publications

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