Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome

doi:10.1186/s12870-016-0787-3

	Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome
	Wang, Yi 1; Liu, Xianju 1,2; Ren, Chong 1; Zhong, Gan-Yuan ; Yang, Long 4; Li, Shaohua1 ; Liang, Zhenchang 1,5
	2016
发表期刊	BMC PLANT BIOLOGY
ISSN	1471-2229
卷号	16
摘要	Background: CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of humans, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific target sites for CRISPR/Cas9 have been computationally identified for several annual model and crop species, but such sites have not been reported for perennial, woody fruit species. In this study, we identified and characterized five types of CRISPR/Cas9 target sites in the widely cultivated grape species Vitis vinifera and developed a user-friendly database for editing grape genomes in the future. Results: A total of 35,767,960 potential CRISPR/Cas9 target sites were identified from grape genomes in this study. Among them, 22,597,817 target sites were mapped to specific genomic locations and 7,269,788 were found to be highly specific. Protospacers and PAMs were found to distribute uniformly and abundantly in the grape genomes. They were present in all the structural elements of genes with the coding region having the highest abundance. Five PAM types, TGG, AGG, GGG, CGG and NGG, were observed. With the exception of the NGG type, they were abundantly present in the grape genomes. Synteny analysis of similar genes revealed that the synteny of protospacers matched the synteny of homologous genes. A user-friendly database containing protospacers and detailed information of the sites was developed and is available for public use at the Grape-CRISPR website (http://biodb.sdau.edu.cn/gc/index.html). Conclusion: Grape genomes harbour millions of potential CRISPR/Cas9 target sites. These sites are widely distributed among and within chromosomes with predominant abundance in the coding regions of genes. We developed a publicly-accessible Grape-CRISPR database for facilitating the use of the CRISPR/Cas9 system as a genome editing tool for functional studies and molecular breeding of grapes. Among other functions, the database allows users to identify and select multi-protospacers for editing similar sequences in grape genomes simultaneously.
关键词	CRISPR/Cas9 Database Genome editing PAM Vitis vinifera
学科领域	Plant Sciences
DOI	10.1186/s12870-016-0787-3
收录类别	SCI
语种	英语
WOS关键词	RNA ; PLANTS ; ENDONUCLEASE ; ARABIDOPSIS ; SEQUENCE ; SYSTEMS ; CAS9 ; TOOL
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000374525800002
出版者	BMC
文献子类	Article
出版地	LONDON
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31572090] ; Hundred Talents of Chinese Academy of Sciences
作者邮箱	shhli@ibcas.ac.cn
作品OA属性	gold, Green Published
引用统计	被引频次：17[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/2S10CLM1/25380
专题	中科院植物分子生理学重点实验室
作者单位	1.Chinese Acad Sci, Beijing Key Lab Grape Sci & Enol, Inst Bot, Beijing 100093, Peoples R China 2.Chinese Acad Sci, Key Lab Plant Resource, Inst Bot, Beijing 100093, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.ARS, USDA, Grape Genet Res Unit, Geneva, NY 14456 USA 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,Liu, Xianju,Ren, Chong,et al. Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome[J]. BMC PLANT BIOLOGY,2016,16.
APA	Wang, Yi.,Liu, Xianju.,Ren, Chong.,Zhong, Gan-Yuan.,Yang, Long.,...&Liang, Zhenchang.(2016).Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome.BMC PLANT BIOLOGY,16.
MLA	Wang, Yi,et al."Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome".BMC PLANT BIOLOGY 16(2016).

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