ArticleG3 (Bethesda, Md.)2019
Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development.
Article in G3 (Bethesda, Md.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
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- Dissection of the Ren6 and Ren7 powdery mildew resistance loci in Vitis piasezkii DVIT2027 using phased parental-progeny genomes and intraspecific locus graph reconstruction.G3 (Bethesda, Md.) · 2025Article
- Evolutionary conservation of the grape sex-determining region in angiosperms and emergence of dioecy in Vitaceae.Nature communications · 2025Article
- Phased T2T genome assemblies facilitate the mining of disease-resistance genes inHorticulture research · 2025Article
- The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired.GigaByte (Hong Kong, China) · 2025Article
- Transcriptome sequencing of seven deep marine invertebrates.Scientific data · 2024Article
- Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation.Horticulture research · 2024Article
- Editorial: Transcriptomics of fruit growth, development and ripening.Frontiers in plant science · 2024Article
- Full-length transcriptome characterization ofFrontiers in genetics · 2024Article
- Proteomic and Low-Polar Metabolite Profiling Reveal Unique Dynamics in Fatty Acid Metabolism during Flower and Berry Development of Table Grapes.International journal of molecular sciences · 2023Article
- Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs.International journal of molecular sciences · 2023Review
- Identification of grapevine clones via high-throughput amplicon sequencing: a proof-of-concept study.G3 (Bethesda, Md.) · 2023Article
- The complete reference genome for grapevine (Horticulture research · 2023Article
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- A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir).G3 (Bethesda, Md.) · 2023Article
- Single-molecule Sequencing of an Animal Mitochondrial Genome Reveals Chloroplast-like Architecture and Repeat-mediated Recombination.Molecular biology and evolution · 2023Article
- Article
- Combination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorization.Scientific reports · 2022Article
- A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis.Genome biology · 2022Article
- 'Nebbiolo' genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.).BMC genomics · 2022Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptomics has been widely applied to study grape berry development. With few exceptions, transcriptomic studies in grape are performed using the available genome sequence, PN40024, as reference. However, differences in gene content among grape accessions, which contribute to phenotypic differences among cultivars, suggest that a single reference genome does not represent the species' entire gene space. Though whole genome assembly and annotation can reveal the relatively unique or "private" gene space of any particular cultivar, transcriptome reconstruction is a more rapid, less costly, and less computationally intensive strategy to accomplish the same goal. In this study, we used single molecule-real time sequencing (SMRT) to sequence full-length cDNA (Iso-Seq) and reconstruct the transcriptome of Cabernet Sauvignon berries during berry ripening. In addition, short reads from ripening berries were used to error-correct low-expression isoforms and to profile isoform expression. By comparing the annotated gene space of Cabernet Sauvignon to other grape cultivars, we demonstrate that the transcriptome reference built with Iso-Seq data represents most of the expressed genes in the grape berries and includes 1,501 cultivar-specific genes. Iso-Seq produced transcriptome profiles similar to those obtained after mapping on a complete genome reference. Together, these results justify the application of Iso-Seq to identify cultivar-specific genes and build a comprehensive reference for transcriptional profiling that circumvents the necessity of a genome reference with its associated costs and computational weight.
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