{"data":{"id":"10.6084/m9.figshare.c.2113961","type":"dois","attributes":{"doi":"10.6084/m9.figshare.c.2113961","prefix":"10.6084","suffix":"m9.figshare.c.2113961","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Yang, Chaojie","givenName":"Chaojie","familyName":"Yang","affiliation":[],"nameIdentifiers":[]},{"name":"Li, Peng","givenName":"Peng","familyName":"Li","affiliation":[],"nameIdentifiers":[]},{"name":"Su, Wenli","givenName":"Wenli","familyName":"Su","affiliation":[],"nameIdentifiers":[]},{"name":"Li, Hao","givenName":"Hao","familyName":"Li","affiliation":[],"nameIdentifiers":[]},{"name":"Liu, Hongbo","givenName":"Hongbo","familyName":"Liu","affiliation":[],"nameIdentifiers":[]},{"name":"Yang, Guang","givenName":"Guang","familyName":"Yang","affiliation":[],"nameIdentifiers":[]},{"name":"Xie, Jing","givenName":"Jing","familyName":"Xie","affiliation":[],"nameIdentifiers":[]},{"name":"Yi, Shengjie","givenName":"Shengjie","familyName":"Yi","affiliation":[],"nameIdentifiers":[]},{"name":"Wang, Jian","givenName":"Jian","familyName":"Wang","affiliation":[],"nameIdentifiers":[]},{"name":"Cui, Xianyan","givenName":"Xianyan","familyName":"Cui","affiliation":[],"nameIdentifiers":[]},{"name":"Wu, Zhihao","givenName":"Zhihao","familyName":"Wu","affiliation":[],"nameIdentifiers":[]},{"name":"Wang, Ligui","givenName":"Ligui","familyName":"Wang","affiliation":[],"nameIdentifiers":[]},{"name":"Hao, Rongzhang","givenName":"Rongzhang","familyName":"Hao","affiliation":[],"nameIdentifiers":[]},{"name":"Jia, Leili","givenName":"Leili","familyName":"Jia","affiliation":[],"nameIdentifiers":[]},{"name":"Qiu, Shaofu","givenName":"Shaofu","familyName":"Qiu","affiliation":[],"nameIdentifiers":[]},{"name":"Song, Hongbin","givenName":"Hongbin","familyName":"Song","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Polymorphism of CRISPR shows separated natural groupings of \u003ci\u003eShigella\u003c/i\u003e subtypes and evidence of horizontal transfer of CRISPR"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2015,"subjects":[{"subject":"Microbiology"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Genetics"},{"subject":"Molecular Biology"},{"subject":"Evolutionary Biology"},{"subject":"Environmental Sciences not elsewhere classified"},{"subject":"Ecology"},{"subject":"Biological Sciences not elsewhere classified"},{"subject":"Infectious Diseases"},{"subject":"FOS: Health sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Computational Biology"}],"contributors":[],"dates":[{"date":"2015-12-05","dateType":"Created"},{"date":"2019-08-19","dateType":"Updated"},{"date":"2015","dateType":"Issued"}],"language":null,"types":{"ris":"GEN","bibtex":"misc","citeproc":"article","schemaOrg":"Collection","resourceType":"Collection","resourceTypeGeneral":"Collection"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"Clustered, regularly interspaced, short palindromic repeats (CRISPR) act as an adaptive RNA-mediated immune mechanism in bacteria. They can also be used for identification and evolutionary studies based on polymorphisms within the CRISPR locus. We amplified and analyzed 6 CRISPR loci from 237 \u003ci\u003eShigella\u003c/i\u003e strains belonging to the 4 species groups, as well as 13 \u003ci\u003eEscherichia coli\u003c/i\u003e strains. The CRISPR-associated (cas) gene sequence arrays of these strains were screened and compared. The CRISPR sequences from \u003ci\u003eShigella\u003c/i\u003e were conserved among subtypes, suggesting that CRISPR may represent a new identification tool for the detection and discrimination of \u003ci\u003eShigella\u003c/i\u003e species. Secondary structure analysis showed a different stem-loop structure at the terminal repeat, suggesting a distinct recognition mechanism in the formation of crRNA. In addition, the presence of “self-target” spacers and polymorphisms within CRISPR in \u003ci\u003eShigella\u003c/i\u003e indicated a selective pressure for inhibition of this system, which has the potential to damage “self DNA.” Homology analysis of spacers showed that CRISPR might be involved in the regulation of virulence transmission. Phylogenetic analysis based on CRISPR sequences from \u003ci\u003eShigella\u003c/i\u003e and \u003ci\u003eE. coli\u003c/i\u003e indicated that although phenotypic properties maintain convergent evolution, the 4 \u003ci\u003eShigella\u003c/i\u003e species do not represent natural groupings. Surprisingly, comparative analysis of \u003ci\u003eShigella\u003c/i\u003e repeats with other species provided new evidence for CRISPR horizontal transfer. Our results suggested that CRISPR analysis is applicable for the detection of \u003ci\u003eShigella\u003c/i\u003e species and for investigation of evolutionary relationships.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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