Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/15/2016
Publication Date: 4/21/2016
Citation: Wang, Y., Liu, X., Ren, C., Zhong, G., Yang, L., Li, S., Liang, Z. 2016. Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome. Biomed Central (BMC) Plant Biology. DOI: 10.1186/x12870-016-0787-3.

Interpretive Summary: A new genomic tool, named as CRISPR/Cas9, has been recently developed to modify genes (genome editing) of a species without leaving any footprint. 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 5 classes, millions of potential CRISPR/Cas9 target sites suitable for genome editing in the widely cultivated grape species Vitis vinifera. We also developed a user-friendly database for grape researchers to explore for editing grape genomes in the future.

Technical Abstract: CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of human, 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. 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 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 coding regions having the highest abundance. Five PAM types, TGG, AGG, GGG, CGG and NGG, were observed and, with the exception of the NGG type, they were abundant 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 detail 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).