In:
PLOS ONE, Public Library of Science (PLoS), Vol. 15, No. 12 ( 2020-12-29), p. e0244515-
Abstract:
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.
Type of Medium:
Online Resource
ISSN:
1932-6203
DOI:
10.1371/journal.pone.0244515
DOI:
10.1371/journal.pone.0244515.g001
DOI:
10.1371/journal.pone.0244515.g002
DOI:
10.1371/journal.pone.0244515.g003
DOI:
10.1371/journal.pone.0244515.g004
DOI:
10.1371/journal.pone.0244515.g005
DOI:
10.1371/journal.pone.0244515.g006
DOI:
10.1371/journal.pone.0244515.t001
DOI:
10.1371/journal.pone.0244515.t002
DOI:
10.1371/journal.pone.0244515.t003
DOI:
10.1371/journal.pone.0244515.t004
DOI:
10.1371/journal.pone.0244515.s001
DOI:
10.1371/journal.pone.0244515.s002
DOI:
10.1371/journal.pone.0244515.s003
DOI:
10.1371/journal.pone.0244515.s004
Language:
English
Publisher:
Public Library of Science (PLoS)
Publication Date:
2020
detail.hit.zdb_id:
2267670-3
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