{"doi":"10.1002/pmic.201700197","title":"Plant Proteogenomics: Improvements to the Grapevine Genome Annotation","abstract":"<jats:title>Abstract</jats:title>\n                  <jats:p>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.</jats:p>","journal":"PROTEOMICS","year":2017,"id":30836,"datarank":1.0639265617990004,"base_score":3.332204510175204,"endowment":3.332204510175204,"self_citation_contribution":0.49983067652628066,"citation_network_contribution":0.5640958852727197,"self_endowment_contribution":0.49983067652628066,"citer_contribution":0.5640958852727197,"corpus_percentile":null,"corpus_rank":null,"citation_count":27,"citer_count":24,"citers_with_citation_signal":21,"citers_with_endowment":21,"datacite_reuse_total":6,"is_dataset":false,"is_dataset_confidence":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":166099,"name":"Matthew Bellgard","orcid":null,"position":1,"is_corresponding":false},{"id":166098,"name":"Brett Chapman","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":3.332204510175204,"endowment":3.332204510175204,"datacite_reuse_total":6,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"28898539","pmcid":null,"openalex_id":"https://openalex.org/W2754860811","authors":[],"funders":[{"funder_name":"Australian Government","grant_id":"","title":null},{"funder_name":"Government of Western 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and Viticultural Research","Fermentation and Sensory Analysis","Plant biochemistry and biosynthesis","Medicine","Biology","Environmental Science","Chromosomes, Plant","Computational Biology","Fruit","Genome, Plant","High-Throughput Nucleotide Sequencing","Humans","Molecular Sequence Annotation","Plant Proteins","Proteogenomics","Proteome","Vitis"],"mesh_terms":["Proteogenomics","Fruit","Humans","Plant Proteins","Genome, Plant","Computational Biology","Proteome","Vitis","Chromosomes, Plant","Molecular Sequence Annotation","High-Throughput Nucleotide Sequencing"],"keywords":["Proteogenomics","Annotation","Computational biology","Genome","Biology","Genome project","Genomics","Genetics","Gene","Vitis vinifera","Bioinformatics","Proteomics"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Industry, innovation and infrastructure"}],"linked_datasets":[{"doi":"10.6084/m9.figshare.16650092.v1","title":"Additional file 3 of Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16650092","title":"Additional file 3 of Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16650107.v1","title":"Additional file 6 of Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16650107","title":"Additional file 6 of Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16650113.v1","title":"Additional file 7 of Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.16650113","title":"Additional file 7 of Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus","publisher":"figshare","resource_type":"JournalArticle"}],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-09T05:23:04.792887Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}