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.
Highlights
Stagonospora nodorum, a fungal ascomycete in the class dothideomycetes, is a damaging pathogen of wheat
The false discovery rate (FDR) for the mass spectra matched against S. nodorum proteins was determined to be 13% by the Mascot decoy method
The flood of genome sequences that are resulting from the wave of "next-generation" sequencing technologies demands the development of time and cost-efficient methods of genome annotation
Summary
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. The prediction of genes from assembled genomic data has traditionally relied on two types of data; sequenced transcripts and homology to gene sequences in related organisms. Based on these data, various in silico methods to predict gene models can be applied. As more and more genome sequences of distantly related nonmodel species become available, the need for efficient, rapid and accurate methods of gene prediction becomes more and more pronounced
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