1. Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants
- Author
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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), and University of Chinese Academy of Sciences [Beijing] (UCAS)
- Subjects
0106 biological sciences ,Computer science ,G-Q ,Computational biology ,PARRs ,01 natural sciences ,Biochemistry ,Genome ,Database ,03 medical and health sciences ,CRISPR/Cas ,Software ,Genome editing ,Software Design ,Genetics ,CRISPR ,Molecular Biology ,030304 developmental biology ,computer.programming_language ,Gene Editing ,0303 health sciences ,Cas9 ,business.industry ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,Computational Mathematics ,Software design ,CRISPR-Cas Systems ,Perl ,business ,computer ,Genome, Plant ,GC-content ,010606 plant biology & botany - 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.
- Published
- 2021