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

Yi Wang; Fatma Lecourieux; Rui Zhang; Zhanwu Dai; David Lecourieux; Shaohua Li; Zhenchang Liang

doi:10.1016/j.gpb.2019.05.008

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

Genomics Proteomics Bioinformatics. 2021 Dec;19(6):937-948. doi: 10.1016/j.gpb.2019.05.008. Epub 2021 Jul 17.

Authors

Yi Wang¹, Fatma Lecourieux², Rui Zhang³, Zhanwu Dai², David Lecourieux², Shaohua Li⁴, Zhenchang Liang⁵

Affiliations

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.
² Ecophysiology and Functional Genomics of Vine, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Institute of Vine and Wine Sciences Bordeaux-Aquitaine, Villenave d'Ornon 33140, France.
³ College of Plant Protection, Shandong Agricultural University, Taian 271018, China.
⁴ University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: shhli@ibcas.ac.cn.
⁵ 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; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China. Electronic address: zl249@ibcas.ac.cn.

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.

Keywords: CRISPR/Cas; Database; G-Q; PAM-rich region; Software.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

CRISPR-Cas Systems*
Gene Editing*
Genome, Plant
Software Design