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

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
	Wang, Yi 1,2; Lecourieux, Fatma 3; Zhang, Rui 4; Dai, Zhanwu3 ; Lecourieux, David 3; Li, Shaohua2 ; Liang, Zhenchang 1,5
	2021
发表期刊	GENOMICS PROTEOMICS & BIOINFORMATICS
ISSN	1672-0229
卷号	19 期号:6 页码:937-948
摘要	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.
关键词	CRISPR/Cas PAM-rich region G-Q Software Database
学科领域	Genetics & Heredity
DOI	10.1016/j.gpb.2019.05.008
收录类别	SCI
语种	英语
WOS关键词	RNA-GUIDED ENDONUCLEASE ; G-QUADRUPLEXES ; CAS9 ; TOOL
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000847852700006
出版者	ELSEVIER
文献子类	Article
出版地	AMSTERDAM
EISSN	2210-3244
资助机构	National Key R&D Program of China [2018YFD1000105] ; National Science Foundation of China [31772266] ; Agricultural Breeding Project of Ningxia Hui Autonomous Region, China [NXNYYZ20150203] ; Hundred Talents of the Chinese Academy of Sciences
作者邮箱	shhli@ibcas.ac.cn ; zl249@ibcas.ac.cn
作品OA属性	gold, Green Published
引用统计	被引频次：2[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/26518
专题	中科院北方资源植物重点实验室
作者单位	1.Chinese Acad Sci, Innovat Acad Seed Design, Beijing Key Lab Grape Sci & Enol, Beijing 100093, Peoples R China 2.Chinese Acad Sci, Innovat Acad Seed Design, CAS Key Lab Plant Resources, Inst Bot, Beijing 100093, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Univ Bordeaux, Inst Vine & Wine Sci Bordeaux Aquitaine, Ecophysiol & Funct Genom Vine, Bordeaux Sci Agro,INRAE, F-33140 Villenave Dornon, France 5.Shandong Agr Univ, Coll Plant Protect, Tai An 271018, Shandong, Peoples R China 6.Chinese Acad Sci, Sino Africa Joint Res Ctr, Wuhan 430074, Peoples R China
推荐引用方式 GB/T 7714	Wang, Yi,Lecourieux, Fatma,Zhang, Rui,et al. Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants[J]. GENOMICS PROTEOMICS & BIOINFORMATICS,2021,19(6):937-948.
APA	Wang, Yi.,Lecourieux, Fatma.,Zhang, Rui.,Dai, Zhanwu.,Lecourieux, David.,...&Liang, Zhenchang.(2021).Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants.GENOMICS PROTEOMICS & BIOINFORMATICS,19(6),937-948.
MLA	Wang, Yi,et al."Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants".GENOMICS PROTEOMICS & BIOINFORMATICS 19.6(2021):937-948.

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