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| Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants | |
Wang, Yi1,2; Lecourieux, Fatma3; Zhang, Rui4; Dai, Zhanwu3 ; Lecourieux, David3; Li, Shaohua2; Liang, Zhenchang1,5
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| 2021 | |
| Source Publication | GENOMICS PROTEOMICS & BIOINFORMATICS
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| ISSN | 1672-0229 |
| Volume | 19Issue:6Pages:937-948 |
| 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. |
| Keyword | CRISPR/Cas PAM-rich region G-Q Software Database |
| Subject Area | Genetics & Heredity |
| DOI | 10.1016/j.gpb.2019.05.008 |
| Indexed By | SCI |
| Language | 英语 |
| WOS Keyword | RNA-GUIDED ENDONUCLEASE ; G-QUADRUPLEXES ; CAS9 ; TOOL |
| WOS Research Area | Science Citation Index Expanded (SCI-EXPANDED) |
| WOS ID | WOS:000847852700006 |
| Publisher | ELSEVIER |
| Subtype | Article |
| Publication Place | AMSTERDAM |
| EISSN | 2210-3244 |
| Funding Organization | 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 |
| Corresponding Author Email | shhli@ibcas.ac.cn ; zl249@ibcas.ac.cn |
| OA | gold, Green Published |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.ibcas.ac.cn/handle/2S10CLM1/26518 |
| Collection | 中科院北方资源植物重点实验室 |
| Affiliation | 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 |
| Recommended Citation 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. |
| Files in This Item: | ||||||
| File Name/Size | DocType | Version | Access | License | ||
| 1-s2.0-S167202292100（1151KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Application Full Text | |
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