ArticleBMC plant biology2016
Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome.
Article in BMC plant biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Advancing CRISPR with deep learning: A comprehensive review of models and databases.Molecular therapy. Nucleic acids · 2025Review
- Genomic resources and genetic improvement of vital tropical and subtropical fruit crops: current status and prospects.AoB PLANTS · 2025Review
- CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis inInternational journal of molecular sciences · 2023Article
- Review
- Genome editing for improving nutritional quality, post-harvest shelf life and stress tolerance of fruits, vegetables, and ornamentals.Frontiers in genome editing · 2023Review
- Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants.Genomics, proteomics & bioinformatics · 2021Article
- Genome editing in fruit, ornamental, and industrial crops.Transgenic research · 2021Review
- Article
- Molecular Tools for Adapting Viticulture to Climate Change.Frontiers in plant science · 2021Review
- CRISPR/Cas9-mediated mutagenesis ofHorticulture research · 2020Article
- Genome-wide identification and analysis of highly specific CRISPR/Cas9 editing sites in pepper (Capsicum annuum L.).PloS one · 2020Article
- Assessment of Cas12a-mediated gene editing efficiency in plants.Plant biotechnology journal · 2019Article
- Article
- Data Mining by Pluralistic Approach on CRISPR Gene Editing in Plants.Frontiers in plant science · 2019Review
- CRISPR/Cas9-mediated efficient targeted mutagenesis in grape in the first generation.Plant biotechnology journal · 2018Article
- CRISPR for Crop Improvement: An Update Review.Frontiers in plant science · 2018Review
- Cultivar-specific gene modulation in Vitis vinifera: analysis of the promoters regulating the expression of WOX transcription factors.Scientific reports · 2017Article
- Breeding next generation tree fruits: technical and legal challenges.Horticulture research · 2017Review
- CRISPR/Cas9 Mediated Genome Engineering for Improvement of Horticultural Crops.Frontiers in plant science · 2017Review
- Use of Natural Diversity and Biotechnology to Increase the Quality and Nutritional Content of Tomato and Grape.Frontiers in plant science · 2017Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of humans, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific target sites for CRISPR/Cas9 have been computationally identified for several annual model and crop species, but such sites have not been reported for perennial, woody fruit species. In this study, we identified and characterized five types of CRISPR/Cas9 target sites in the widely cultivated grape species Vitis vinifera and developed a user-friendly database for editing grape genomes in the future.
resultsA total of 35,767,960 potential CRISPR/Cas9 target sites were identified from grape genomes in this study. Among them, 22,597,817 target sites were mapped to specific genomic locations and 7,269,788 were found to be highly specific. Protospacers and PAMs were found to distribute uniformly and abundantly in the grape genomes. They were present in all the structural elements of genes with the coding region having the highest abundance. Five PAM types, TGG, AGG, GGG, CGG and NGG, were observed. With the exception of the NGG type, they were abundantly present in the grape genomes. Synteny analysis of similar genes revealed that the synteny of protospacers matched the synteny of homologous genes. A user-friendly database containing protospacers and detailed information of the sites was developed and is available for public use at the Grape-CRISPR website ( http://biodb.sdau.edu.cn/gc/index.html ).
conclusionGrape genomes harbour millions of potential CRISPR/Cas9 target sites. These sites are widely distributed among and within chromosomes with predominant abundance in the coding regions of genes. We developed a publicly-accessible Grape-CRISPR database for facilitating the use of the CRISPR/Cas9 system as a genome editing tool for functional studies and molecular breeding of grapes. Among other functions, the database allows users to identify and select multi-protospacers for editing similar sequences in grape genomes simultaneously.
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