Centre for Comparative Genomics, Murdoch University, Western Australia, Australia.
Proteomics. 2017 Nov;17(21). doi: 10.1002/pmic.201700197. Epub 2017 Oct 13.
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.
葡萄藤是葡萄酒行业的重要多年生水果，其一些病原体已被证明可降低心脏病的发病率，因此对健康行业也有影响。自葡萄品种黑比诺的测序和组装以来，已有几项研究为其基因组注释做出了贡献。这项新的研究通过使用来自 CRIBI 的最新基因组注释、来自品种赤霞珠的遗留蛋白质组数据集和大型 RNA-seq 数据集进行蛋白质基因组学分析，进一步为基因组注释工作做出了贡献。共鉴定出 341 个新的注释事件，包括 5 个移码、37 个翻译的 UTR、15 个外显子边界、1 个新剪接、9 个新外显子、159 个基因边界、112 条反向链和 213 个基因和 323 个蛋白质中的 11 个新基因事件。通过蛋白质基因组学证据，Augustus 基因预测工具预测了 52 个新的和修订的基因（54 个蛋白异构体），其中 11 个基因与关键性状相关，如应激耐受和花香型葡萄酒的特征。这项研究还强调了与基因组的可能过度组装，特别是在第 7 号染色体上。
