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

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

作者机构：Beijing Key Laboratory of Grape Science and Enologyand CAS Key Laboratory of Plant ResourcesInstitute of Botanythe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing 100093China University of Chinese Academy of SciencesBeijing 100049China Ecophysiology and Functional Genomics of VineBordeaux Sciences AgroINRAEUniversity of BordeauxInstitute of Vine and Wine Sciences Bordeaux-AquitaineVillenave d’Ornon 33140France College of Plant ProtectionShandong Agricultural UniversityTaian 271018China Sino-Africa Joint Research CenterChinese Academy of SciencesWuhan 430074China 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2021年第19卷第6期

页      面：937-948页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 09[农学] 071007[理学-遗传学] 0901[农学-作物学] 090102[农学-作物遗传育种] 

基　　金：supported by grants from the National Key R&D Program of China (Grant No. 2018YFD1000105) the National Science Foundation of China (Grant No. 31772266) the Agricultural Breeding Project of Ningxia Hui Autonomous Region, China (Grant No. NXNYYZ20150203) the Hundred Talents of the Chinese Academy of Sciences 

主　　题：CRISPR/Cas PAM-rich region G-Q Software Database 

摘      要：CRISPR-based genome editing systems have been successfully and effectively used in many ***,only a few studies have reported the comparison between CRISPR/Cas9 and CRISPR/Cpf1 systems in the whole-genome *** many web-based toolkits are available,there is still a shortage of comprehensive,user-friendly,and plant-specific CRISPR databases and desktop *** 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)*** this information,we built a comprehensive CRISPR database(including 138 plant genome data sources,***/pc/***),which provides search tools for the identification of CRISPR editing sites in both CRISPR/Cas9 and CRISPR/Cpf1 *** 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 ***,this study provides helpful data and software for easy selection and application of CRISPR-based genome editing systems in plants.