Plant Proteogenomics: Improvements to the Grapevine Genome Annotation.
Identifieur interne : 000305 ( Main/Exploration ); précédent : 000304; suivant : 000306Plant Proteogenomics: Improvements to the Grapevine Genome Annotation.
Auteurs : Brett Chapman [Australie] ; Matthew Bellgard [Australie]Source :
- Proteomics [ 1615-9861 ] ; 2017.
Descripteurs français
- KwdFr :
- Annotation de séquence moléculaire (MeSH), Biologie informatique (méthodes), Chromosomes de plante (MeSH), Fruit (génétique), Fruit (métabolisme), Génome végétal (MeSH), Humains (MeSH), Protéines végétales (analyse), Protéines végétales (génétique), Protéogénomique (MeSH), Protéome (analyse), Séquençage nucléotidique à haut débit (méthodes), Vitis (croissance et développement), Vitis (génétique), Vitis (métabolisme).
- MESH :
- analyse : Protéines végétales, Protéome.
- croissance et développement : Vitis.
- génétique : Fruit, Protéines végétales, Vitis.
- métabolisme : Fruit, Vitis.
- méthodes : Biologie informatique, Séquençage nucléotidique à haut débit.
- Annotation de séquence moléculaire, Chromosomes de plante, Génome végétal, Humains, Protéogénomique.
English descriptors
- KwdEn :
- Chromosomes, Plant (MeSH), Computational Biology (methods), Fruit (genetics), Fruit (metabolism), Genome, Plant (MeSH), High-Throughput Nucleotide Sequencing (methods), Humans (MeSH), Molecular Sequence Annotation (MeSH), Plant Proteins (analysis), Plant Proteins (genetics), Proteogenomics (MeSH), Proteome (analysis), Vitis (genetics), Vitis (growth & development), Vitis (metabolism).
- MESH :
- chemical , analysis : Plant Proteins, Proteome.
- genetics : Fruit, Plant Proteins, Vitis.
- growth & development : Vitis.
- metabolism : Fruit, Vitis.
- methods : Computational Biology, High-Throughput Nucleotide Sequencing.
- Chromosomes, Plant, Genome, Plant, Humans, Molecular Sequence Annotation, Proteogenomics.
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.
DOI: 10.1002/pmic.201700197
PubMed: 28898539
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28898539</PMID><DateCompleted><Year>2018</Year><Month>05</Month><Day>23</Day></DateCompleted><DateRevised><Year>2018</Year><Month>05</Month><Day>23</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1615-9861</ISSN><JournalIssue CitedMedium="Internet"><Volume>17</Volume><Issue>21</Issue><PubDate><Year>2017</Year><Month>Nov</Month></PubDate></JournalIssue><Title>Proteomics</Title><ISOAbbreviation>Proteomics</ISOAbbreviation></Journal><ArticleTitle>Plant Proteogenomics: Improvements to the Grapevine Genome Annotation.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1002/pmic.201700197</ELocationID><Abstract><AbstractText>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.</AbstractText><CopyrightInformation>© 2017 WILEY-VCH Verlag GmbH & Co. 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