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Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants
Genomics, Proteomics & Bioinformatics ( IF 9.5 ) Pub Date : 2021-07-17 , DOI: 10.1016/j.gpb.2019.05.008
Yi Wang 1 , Fatma Lecourieux 2 , Rui Zhang 3 , Zhanwu Dai 2 , David Lecourieux 2 , Shaohua Li 4 , Zhenchang Liang 5
Affiliation  

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.



中文翻译:

数据比较和软件设计,便于在植物中选择和应用基于 CRISPR 的基因组编辑系统

基于 CRISPR 的基因组编辑系统已成功有效地用于许多生物体中。然而,只有少数研究报道了CRISPR/Cas 9 和 CRISPR/Cpf1 系统在全基因组应用中的比较。尽管有许多基于网络的工具包可用,但仍然缺乏全面的、用户友好的和植物特定的 CRISPR数据库和桌面软件。在本研究中,我们通过考虑原始间隔区相邻基序 (PAM) 位点的丰度、GC 含量的影响、最佳原始间隔区长度、潜在的普遍性,确定并分析了 CRISPR/Cas9 和 CRISPR/Cpf1 系统之间的异同。在植物界,富含 PAM 的地区(PARR) 抑制率,以及 G-四链体 ( GQ ) 结构的影响。利用这些信息,我们建立了一个全面的 CRISPR 数据库(包括 138 个植物基因组数据源,www.grapeworld.cn/pc/index.html),它为识别 CRISPR/Cas9 和 CRISPR/ 中的 CRISPR 编辑位点提供了搜索工具。 Cpf1 系统。我们还在Perl/Tk工具的基础上开发了一款桌面软件,方便和改进了Linux和/或Windows平台上全基因组水平的CRISPR编辑位点的检测和分析。因此,本研究为在植物中轻松选择和应用基于 CRISPR 的基因组编辑系统提供了有用的数据和软件。

更新日期:2021-07-17
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