Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants
- Author:
Wang YI
1
;
Lecourieux FATMA
;
Zhang RUI
;
Dai ZHANWU
;
Lecourieux DAVID
;
Li SHAOHUA
;
Liang ZHENCHANG
Author Information
1. Beijing Key Laboratory of Grape Science and Enology,and CAS Key Laboratory of Plant Resources,Institute of Botany,the Innovative Academy of Seed Design,Chinese Academy of Sciences,Beijing 100093,China;University of Chinese Academy of Sciences,Beijing 100049,China
- Keywords:
CRISPR/Cas;
PAM-rich region;
G-Q;
Software;
Database
- From:
Genomics, Proteomics & Bioinformatics
2021;19(6):937-948
- CountryChina
- Language:Chinese
-
Abstract:
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, the effects of GC content, optimal proto-spacer length, potential universality within the plant kingdom, PAM-rich region (PARR) inhibiting ratio, and the 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 the 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.
