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A proteogenomic update to Yersinia: enhancing genome annotation
Samuel H Payne1, Shih-Ting Huang, Rembert Pieper
1J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA. spayne@jcvi.org
BMC Genomics
|August 7, 2010
Summary
Proteogenomics rapidly improves genome annotation accuracy by integrating experimental proteomics data. This study enhanced the Yersinia pestis genome, correcting gene models and improving signal peptide identification.
Area of Science:
- Genomics
- Proteomics
- Bioinformatics
Background:
- Accurate genome annotation is crucial for biomedical research.
- Rapid sequencing generates vast genomic data, often leading to annotation errors.
- Existing gene sets contain inaccuracies in protein primary structures.
Purpose of the Study:
- To apply proteogenomics for accurate genome annotation of Yersinia pestis.
- To identify and correct misannotations in the Yersinia pestis genome.
- To enhance genome annotation across related Yersinia species.
Main Methods:
- Comprehensive proteogenomic analysis of Yersinia pestis KIM.
- Utilizing experimental proteomics data to validate and correct gene models.
- Applying findings to annotate 21 additional Yersinia genomes.
Main Results:
- Discovered non-annotated genes and corrected protein boundaries.
- Removed erroneously annotated open reading frames (ORFs).
- Made significant progress in accurately identifying signal peptides.
- Successfully corrected and enhanced annotations for 21 Yersinia genomes.
Conclusions:
- 141 gene models were updated in RefSeq and GenBank.
- Improved gene models are accessible via NCBI tools.
- New, more accurate methods for identifying signal peptides in proteomics data were discovered.
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