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Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants

Authors :
Zhanwu Dai
Fatma Lecourieux
Yi Wang
Shaohua Li
David Lecourieux
Rui Zhang
Zhenchang Liang
Beijing Key Laboratory of Grape Science and Enology/CAS Key Laboratory of Plant Resource
Institute of Botany [Beijing] (IB-CAS)
Chinese Academy of Sciences [Beijing] (CAS)-Chinese Academy of Sciences [Beijing] (CAS)
Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV)
Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Shandong Agricultural University (SDAU)
University of Chinese Academy of Sciences [Beijing] (UCAS)
Source :
Genomics, Proteomics and Bioinformatics, Genomics, Proteomics and Bioinformatics, Elsevier, In press, ⟨10.1016/j.gpb.2019.05.008⟩
Publication Year :
2021
Publisher :
Elsevier BV, 2021.

Abstract

International audience; CRISPR-based genome editing systems have been successfully and effectively used in many organisms. However, only a few studies have reported the comparison between CRISPR/Cas9 and CRISPR/Cpf1 systems in the whole-genome applications. Although many web-based toolkits are available, there is still a shortage of comprehensive, user-friendly, and plant-specific CRISPR databases and desktop software. In this study, we identified and analyzed the similarities and differences between CRISPR/Cas9 and CRISPR/Cpf1 systems by considering the abundance of proto-spacer adjacent motif (PAM) sites, effects of GC content, optimal proto-spacer length, potential universality within the plant kingdom, PAM-rich region (PARR) inhibiting ratio, and effects of G-quadruplex (G-Q) structures. Using this information, we built a comprehensive CRISPR database (including 138 plant genome data sources, www.grapeworld.cn/pc/index.html), which provides search tools for the identification of CRISPR editing sites in both CRISPR/Cas9 and CRISPR/Cpf1 systems. We also developed a desktop software on the basis of Perl/TK tool, which facilitates and improves the detection and analysis of CRISPR editing sites at the whole-genome level on Linux and/or Windows platform. Therefore, this study provides helpful data and software for easy selection and application of CRISPR-based genome editing systems in plants.

Details

ISSN :
16720229
Volume :
19
Database :
OpenAIRE
Journal :
Genomics, Proteomics & Bioinformatics
Accession number :
edsair.doi.dedup.....ec8486c13f52c8be7ce2e781a804c1f6
Full Text :
https://doi.org/10.1016/j.gpb.2019.05.008