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

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 s...

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Autores principales: Wang, Yi, Lecourieux, Fatma, Zhang, Rui, Dai, Zhanwu, Lecourieux, David, Li, Shaohua, Liang, Zhenchang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9402788/
https://www.ncbi.nlm.nih.gov/pubmed/34280549
http://dx.doi.org/10.1016/j.gpb.2019.05.008
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author Wang, Yi
Lecourieux, Fatma
Zhang, Rui
Dai, Zhanwu
Lecourieux, David
Li, Shaohua
Liang, Zhenchang
author_facet Wang, Yi
Lecourieux, Fatma
Zhang, Rui
Dai, Zhanwu
Lecourieux, David
Li, Shaohua
Liang, Zhenchang
author_sort Wang, Yi
collection PubMed
description 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.
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spelling pubmed-94027882022-08-26 Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants Wang, Yi Lecourieux, Fatma Zhang, Rui Dai, Zhanwu Lecourieux, David Li, Shaohua Liang, Zhenchang Genomics Proteomics Bioinformatics Original Research 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. Elsevier 2021-12 2021-07-17 /pmc/articles/PMC9402788/ /pubmed/34280549 http://dx.doi.org/10.1016/j.gpb.2019.05.008 Text en © 2021 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Original Research
Wang, Yi
Lecourieux, Fatma
Zhang, Rui
Dai, Zhanwu
Lecourieux, David
Li, Shaohua
Liang, Zhenchang
Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants
title Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants
title_full Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants
title_fullStr Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants
title_full_unstemmed Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants
title_short Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants
title_sort data comparison and software design for easy selection and application of crispr-based genome editing systems in plants
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9402788/
https://www.ncbi.nlm.nih.gov/pubmed/34280549
http://dx.doi.org/10.1016/j.gpb.2019.05.008
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