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Genome-wide identification and analysis of highly specific CRISPR/Cas9 editing sites in pepper (Capsicum annuum L.)

The CRISPR/Cas9 system is an efficient genome editing tool that possesses the outstanding advantages of simplicity and high efficiency. Genome-wide identification and specificity analysis of editing sites is an effective approach for mitigating the risk of off-target effects of CRISPR/Cas9 and has b...

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Autores principales: Li, Guanliang, Zhou, Ziyan, Liang, Lingrui, Song, Zhao, Hu, Yafei, Cui, Junjie, Chen, Weili, Hu, Kailin, Cheng, Jiaowen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7771699/
https://www.ncbi.nlm.nih.gov/pubmed/33373406
http://dx.doi.org/10.1371/journal.pone.0244515
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author Li, Guanliang
Zhou, Ziyan
Liang, Lingrui
Song, Zhao
Hu, Yafei
Cui, Junjie
Chen, Weili
Hu, Kailin
Cheng, Jiaowen
author_facet Li, Guanliang
Zhou, Ziyan
Liang, Lingrui
Song, Zhao
Hu, Yafei
Cui, Junjie
Chen, Weili
Hu, Kailin
Cheng, Jiaowen
author_sort Li, Guanliang
collection PubMed
description The CRISPR/Cas9 system is an efficient genome editing tool that possesses the outstanding advantages of simplicity and high efficiency. Genome-wide identification and specificity analysis of editing sites is an effective approach for mitigating the risk of off-target effects of CRISPR/Cas9 and has been applied in several plant species but has not yet been reported in pepper. In present study, we first identified genome-wide CRISPR/Cas9 editing sites based on the ‘Zunla-1’ reference genome and then evaluated the specificity of CRISPR/Cas9 editing sites through whole-genome alignment. Results showed that a total of 603,202,314 CRISPR/Cas9 editing sites, including 229,909,837 (~38.11%) NGG-PAM sites and 373,292,477 (~61.89%) NAG-PAM sites, were detectable in the pepper genome, and the systematic characterization of their composition and distribution was performed. Furthermore, 29,623,855 highly specific NGG-PAM sites were identified through whole-genome alignment analysis. There were 26,699,38 (~90.13%) highly specific NGG-PAM sites located in intergenic regions, which was 9.13 times of the number in genic regions, but the average density in genic regions was higher than that in intergenic regions. More importantly, 34,251 (~96.93%) out of 35,336 annotated genes exhibited at least one highly specific NGG-PAM site in their exons, and 90.50% of the annotated genes exhibited at least 4 highly specific NGG- PAM sites, indicating that the set of highly specific CRISPR/Cas9 editing sites identified in this study was widely applicable and conducive to the minimization of the off-target effects of CRISPR/Cas9 in pepper.
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spelling pubmed-77716992021-01-08 Genome-wide identification and analysis of highly specific CRISPR/Cas9 editing sites in pepper (Capsicum annuum L.) Li, Guanliang Zhou, Ziyan Liang, Lingrui Song, Zhao Hu, Yafei Cui, Junjie Chen, Weili Hu, Kailin Cheng, Jiaowen PLoS One Research Article The CRISPR/Cas9 system is an efficient genome editing tool that possesses the outstanding advantages of simplicity and high efficiency. Genome-wide identification and specificity analysis of editing sites is an effective approach for mitigating the risk of off-target effects of CRISPR/Cas9 and has been applied in several plant species but has not yet been reported in pepper. In present study, we first identified genome-wide CRISPR/Cas9 editing sites based on the ‘Zunla-1’ reference genome and then evaluated the specificity of CRISPR/Cas9 editing sites through whole-genome alignment. Results showed that a total of 603,202,314 CRISPR/Cas9 editing sites, including 229,909,837 (~38.11%) NGG-PAM sites and 373,292,477 (~61.89%) NAG-PAM sites, were detectable in the pepper genome, and the systematic characterization of their composition and distribution was performed. Furthermore, 29,623,855 highly specific NGG-PAM sites were identified through whole-genome alignment analysis. There were 26,699,38 (~90.13%) highly specific NGG-PAM sites located in intergenic regions, which was 9.13 times of the number in genic regions, but the average density in genic regions was higher than that in intergenic regions. More importantly, 34,251 (~96.93%) out of 35,336 annotated genes exhibited at least one highly specific NGG-PAM site in their exons, and 90.50% of the annotated genes exhibited at least 4 highly specific NGG- PAM sites, indicating that the set of highly specific CRISPR/Cas9 editing sites identified in this study was widely applicable and conducive to the minimization of the off-target effects of CRISPR/Cas9 in pepper. Public Library of Science 2020-12-29 /pmc/articles/PMC7771699/ /pubmed/33373406 http://dx.doi.org/10.1371/journal.pone.0244515 Text en © 2020 Li et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Li, Guanliang
Zhou, Ziyan
Liang, Lingrui
Song, Zhao
Hu, Yafei
Cui, Junjie
Chen, Weili
Hu, Kailin
Cheng, Jiaowen
Genome-wide identification and analysis of highly specific CRISPR/Cas9 editing sites in pepper (Capsicum annuum L.)
title Genome-wide identification and analysis of highly specific CRISPR/Cas9 editing sites in pepper (Capsicum annuum L.)
title_full Genome-wide identification and analysis of highly specific CRISPR/Cas9 editing sites in pepper (Capsicum annuum L.)
title_fullStr Genome-wide identification and analysis of highly specific CRISPR/Cas9 editing sites in pepper (Capsicum annuum L.)
title_full_unstemmed Genome-wide identification and analysis of highly specific CRISPR/Cas9 editing sites in pepper (Capsicum annuum L.)
title_short Genome-wide identification and analysis of highly specific CRISPR/Cas9 editing sites in pepper (Capsicum annuum L.)
title_sort genome-wide identification and analysis of highly specific crispr/cas9 editing sites in pepper (capsicum annuum l.)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7771699/
https://www.ncbi.nlm.nih.gov/pubmed/33373406
http://dx.doi.org/10.1371/journal.pone.0244515
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