Journal article
Plant Proteogenomics: Improvements to the Grapevine Genome Annotation
Proteomics, Vol.17(21)
2017
Abstract
Grapevine is an important perennial fruit to the wine industry, and has implications for the health industry with some causative agents proven to reduce heart disease. Since the sequencing and assembly of grapevine cultivar Pinot Noir, several studies have contributed to its genome annotation. This new study further contributes toward genome annotation efforts by conducting a proteogenomics analysis using the latest genome annotation from CRIBI, legacy proteomics dataset from cultivar Cabernet Sauvignon and a large RNA-seq dataset. A total of 341 novel annotation events are identified consisting of five frame-shifts, 37 translated UTRs, 15 exon boundaries, one novel splice, nine novel exons, 159 gene boundaries, 112 reverse strands, and one novel gene event in 213 genes and 323 proteins. From this proteogenomics evidence, the Augustus gene prediction tool predicted 52 novel and revised genes (54 protein isoforms), 11 genes of which are associated with key traits such as stress tolerance and floral and fruity wine characteristics. This study also highlights a likely over-assembly with the genome, particularly on chromosome 7.
Details
- Title
- Plant Proteogenomics: Improvements to the Grapevine Genome Annotation
- Authors/Creators
- B. Chapman (Author/Creator) - Murdoch UniversityM. Bellgard (Author/Creator) - Murdoch University
- Publication Details
- Proteomics, Vol.17(21)
- Publisher
- John Wiley & Sons Ltd.
- Identifiers
- 991005540157507891
- Copyright
- © 2017 John Wiley & Sons, Inc.
- Murdoch Affiliation
- Centre for Comparative Genomics
- Language
- English
- Resource Type
- Journal article
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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
- Biochemistry & Molecular Biology
- ESI research areas
- Biology & Biochemistry