ArticleBMC genomics2013
De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
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- Assessment of 'Cabernet Sauvignon' Grape Quality Half-Véraison to Maturity for Grapevines Grown in Different Regions.International journal of molecular sciences · 2023Article
- Differentially expression analyses in fruit of cultivated and wild species of grape and peach.Scientific reports · 2023Article
- Identification of Key Genes Induced by Different Potassium Levels Provides Insight into the Formation of Fruit Quality in Grapes.International journal of molecular sciences · 2023Article
- Glutathione S-transferase: a candidate gene for berry color in muscadine grapes (Vitis rotundifolia).G3 (Bethesda, Md.) · 2022Article
- 'Nebbiolo' genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.).BMC genomics · 2022Article
- Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits.Frontiers in plant science · 2022Article
- The grapevine (Vitis vinifera L.) floral transcriptome in Pinot noir variety: identification of tissue-related gene networks and whorl-specific markers in pre- and post-anthesis phases.Horticulture research · 2021Article
- Rootstock influences the effect of grapevine leafroll-associated viruses on berry development and metabolism via abscisic acid signalling.Molecular plant pathology · 2021Article
- Transcriptomic and metabolomic joint analysis reveals distinct flavonoid biosynthesis regulation for variegated testa color development in peanut (Arachis hypogaea L.).Scientific reports · 2021Article
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- Transcriptomic and biochemical investigations support the role of rootstock-scion interaction in grapevine berry quality.BMC genomics · 2020Article
- Recent advances in biotechnological studies on wild grapevines as valuable resistance sources for smart viticulture.Molecular biology reports · 2020Review
- Identification and functional characterization of thePlant signaling & behavior · 2020Article
- Comparative (Within Species) Genomics of theFrontiers in genetics · 2020Article
- Diploid Genome Assembly of the Wine Grape Carménère.G3 (Bethesda, Md.) · 2019Article
- Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development.G3 (Bethesda, Md.) · 2019Article
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPlants such as grapevine (Vitis spp.) display significant inter-cultivar genetic and phenotypic variation. The genetic components underlying phenotypic diversity in grapevine must be understood in order to disentangle genetic and environmental factors.
resultsWe have shown that cDNA sequencing by RNA-seq is a robust approach for the characterization of varietal diversity between a local grapevine cultivar (Corvina) and the PN40024 reference genome. We detected 15,161 known genes including 9463 with novel splice isoforms, and identified 2321 potentially novel protein-coding genes in non-annotated or unassembled regions of the reference genome. We also discovered 180 apparent private genes in the Corvina genome which were missing from the reference genome.
conclusionsThe de novo assembly approach allowed a substantial amount of the Corvina transcriptome to be reconstructed, improving known gene annotations by robustly defining gene structures, annotating splice isoforms and detecting genes without annotations. The private genes we discovered are likely to be nonessential but could influence certain cultivar-specific characteristics. Therefore, the application of de novo transcriptome assembly should not be restricted to species lacking a reference genome because it can also improve existing reference genome annotations and identify novel, cultivar-specific genes.
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