Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome
文献类型：期刊论文
| 作者 | Wang, Yi3; Liu, Xianju3,4; Ren, Chong3; Zhong, Gan-Yuan; Yang, Long1; Li, Shaohua3 ; Liang, Zhenchang3,6
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| 刊名 | BMC PLANT BIOLOGY
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| 出版日期 | 2016 |
| 卷号 | 16 |
| 关键词 | CRISPR/Cas9 Database Genome editing PAM Vitis vinifera |
| ISSN号 | 1471-2229 |
| DOI | 10.1186/s12870-016-0787-3 |
| 文献子类 | Article |
| 英文摘要 | 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. |
| 学科主题 | Plant Sciences |
| 出版地 | LONDON |
| WOS关键词 | RNA ; PLANTS ; ENDONUCLEASE ; ARABIDOPSIS ; SEQUENCE ; SYSTEMS ; CAS9 ; TOOL |
| WOS研究方向 | Science Citation Index Expanded (SCI-EXPANDED) |
| 语种 | 英语 |
| WOS记录号 | WOS:000374525800002 |
| 出版者 | BMC |
| 资助机构 | National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31572090] ; Hundred Talents of Chinese Academy of Sciences |
| 源URL | [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.ARS, USDA, Grape Genet Res Unit, Geneva, NY 14456 USA 2.Chinese Acad Sci, Sino Africa Joint Res Ctr, Wuhan 430074, Peoples R China 3.Chinese Acad Sci, Beijing Key Lab Grape Sci & Enol, Inst Bot, Beijing 100093, Peoples R China 4.Chinese Acad Sci, Key Lab Plant Resource, Inst Bot, Beijing 100093, Peoples R China 5.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 6.Shandong Agr Univ, Coll Plant Protect, Tai An 271018, Shandong, 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). |
入库方式： OAI收割
来源：植物研究所
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