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


CONCLUSIONS
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.
Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. China.
Yi
Y
Wang
Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. China.|University of Chinese Academy of Sciences, Beijing, 100049, P.R. China.
Xianju
X
Liu
Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. China.
Chong
C
Ren
USDA-ARS Grape Genetics Research Unit, Geneva, NY, 14456, USA.
Gan-Yuan
GY
Zhong
College of Plant Protection, Shandong Agricultural University, Taian, 271018, China.
Long
L
Yang
Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. China. shhli@ibcas.ac.cn.
Shaohua
S
Li
Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. China.|Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
Zhenchang
Z
Liang
D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D064113:CRISPR-Cas Systems / Q000235:genetics*; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D030561:Databases, Nucleic Acid; D005091:Exons / Q000235:genetics; D000072669:Gene Editing; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D020407:Internet; D007438:Introns / Q000235:genetics; D020506:Untranslated Regions / Q000235:genetics; D027843:Vitis / Q000235:genetics*
D020506:Untranslated Regions
CRISPR/Cas9; Database; Genome editing; PAM; Vitis vinifera