Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome
Identifieur interne : 000169 ( Main/Exploration ); précédent : 000168; suivant : 000170Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome
Auteurs : Yi Wang [République populaire de Chine] ; Xianju Liu [République populaire de Chine] ; Chong Ren [République populaire de Chine] ; Gan-Yuan Zhong [États-Unis] ; Long Yang [République populaire de Chine] ; Shaohua Li [République populaire de Chine] ; Zhenchang Liang [République populaire de Chine]Source :
- BMC Plant Biology [ 1471-2229 ] ; 2016.
Abstract
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
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 (
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.
The online version of this article (doi:10.1186/s12870-016-0787-3) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12870-016-0787-3
PubMed: 27098585
PubMed Central: 4839089
Affiliations:
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Le document en format XML
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China</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Liu, Xianju" sort="Liu, Xianju" uniqKey="Liu X" first="Xianju" last="Liu">Xianju Liu</name><affiliation wicri:level="3"><nlm:aff id="Aff1">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</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="Aff2">University of Chinese Academy of Sciences, Beijing, 100049 P.R. China</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>University of Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Ren, Chong" sort="Ren, Chong" uniqKey="Ren C" first="Chong" last="Ren">Chong Ren</name><affiliation wicri:level="3"><nlm:aff id="Aff1">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</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhong, Gan Yuan" sort="Zhong, Gan Yuan" uniqKey="Zhong G" first="Gan-Yuan" last="Zhong">Gan-Yuan Zhong</name><affiliation wicri:level="2"><nlm:aff id="Aff3">USDA-ARS Grape Genetics Research Unit, Geneva, NY 14456 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">État de New York</region></placeName><wicri:cityArea>USDA-ARS Grape Genetics Research Unit, Geneva</wicri:cityArea></affiliation></author><author><name sortKey="Yang, Long" sort="Yang, Long" uniqKey="Yang L" first="Long" last="Yang">Long Yang</name><affiliation wicri:level="1"><nlm:aff id="Aff4">College of Plant Protection, Shandong Agricultural University, Taian, 271018 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Plant Protection, Shandong Agricultural University, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation></author><author><name sortKey="Li, Shaohua" sort="Li, Shaohua" uniqKey="Li S" first="Shaohua" last="Li">Shaohua Li</name><affiliation wicri:level="3"><nlm:aff id="Aff1">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</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Liang, Zhenchang" sort="Liang, Zhenchang" uniqKey="Liang Z" first="Zhenchang" last="Liang">Zhenchang Liang</name><affiliation wicri:level="3"><nlm:aff id="Aff1">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</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff5">Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Plant Biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>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 <italic>Vitis vinifera</italic> and developed a user-friendly database for editing grape genomes in the future.</p></sec><sec><title>Results</title><p>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 (<ext-link ext-link-type="uri" xlink:href="http://biodb.sdau.edu.cn/gc/index.html">http://biodb.sdau.edu.cn/gc/index.html</ext-link>).</p></sec><sec><title>Conclusion</title><p>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.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12870-016-0787-3) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Jinek, M" uniqKey="Jinek M">M Jinek</name></author><author><name sortKey="Chylinski, K" uniqKey="Chylinski K">K Chylinski</name></author><author><name sortKey="Fonfara, I" uniqKey="Fonfara I">I Fonfara</name></author><author><name sortKey="Hauer, M" uniqKey="Hauer M">M Hauer</name></author><author><name sortKey="Doudna, Ja" uniqKey="Doudna J">JA Doudna</name></author><author><name sortKey="Charpentier, E" uniqKey="Charpentier E">E Charpentier</name></author></analytic></biblStruct><biblStruct><analytic><author><name 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Noel</name></author><author><name sortKey="Policriti, A" uniqKey="Policriti A">A Policriti</name></author><author><name sortKey="Clepet, C" uniqKey="Clepet C">C Clepet</name></author><author><name sortKey="Casagrande, A" uniqKey="Casagrande A">A Casagrande</name></author><author><name sortKey="Choisne, N" uniqKey="Choisne N">N Choisne</name></author><author><name sortKey="Aubourg, S" uniqKey="Aubourg S">S Aubourg</name></author><author><name sortKey="Vitulo, N" uniqKey="Vitulo N">N Vitulo</name></author><author><name sortKey="Jubin, C" uniqKey="Jubin C">C Jubin</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>État de New York</li></region><settlement><li>Pékin</li></settlement></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Wang, Yi" sort="Wang, Yi" uniqKey="Wang Y" first="Yi" last="Wang">Yi Wang</name></noRegion><name sortKey="Li, Shaohua" sort="Li, Shaohua" uniqKey="Li S" first="Shaohua" last="Li">Shaohua Li</name><name sortKey="Liang, Zhenchang" sort="Liang, Zhenchang" uniqKey="Liang Z" first="Zhenchang" last="Liang">Zhenchang Liang</name><name sortKey="Liang, Zhenchang" sort="Liang, Zhenchang" uniqKey="Liang Z" first="Zhenchang" last="Liang">Zhenchang Liang</name><name sortKey="Liu, Xianju" sort="Liu, Xianju" uniqKey="Liu X" first="Xianju" last="Liu">Xianju Liu</name><name sortKey="Liu, Xianju" sort="Liu, Xianju" uniqKey="Liu X" first="Xianju" last="Liu">Xianju Liu</name><name sortKey="Ren, Chong" sort="Ren, Chong" uniqKey="Ren C" first="Chong" last="Ren">Chong Ren</name><name sortKey="Yang, Long" sort="Yang, Long" uniqKey="Yang L" first="Long" last="Yang">Long Yang</name></country><country name="États-Unis"><region name="État de New York"><name sortKey="Zhong, Gan Yuan" sort="Zhong, Gan Yuan" uniqKey="Zhong G" first="Gan-Yuan" last="Zhong">Gan-Yuan Zhong</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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