title: A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs.
abstract: Motivation. Clustered regularly interspaced short palindromic repeat (CRISPR) is a genetic element with active regulation roles for foreign invasive genes in the prokaryotic genomes and has been engineered to work with the CRISPR-associated sequence (Cas) gene Cas9 as one of the modern genome editing technologies. Due to inconsistent definitions, the existing CRISPR detection programs seem to have missed some weak CRISPR signals. Results. This study manually curates all the currently annotated CRISPR elements in the prokaryotic genomes and proposes 95 updates to the annotations. A new definition is proposed to cover all the CRISPRs. The comprehensive comparison of CRISPR numbers on the taxonomic levels of both domains and genus shows high variations for closely related species even in the same genus. The detailed investigation of how CRISPRs are evolutionarily manipulated in the 8 completely sequenced species in the genus Thermoanaerobacter demonstrates that transposons act as a frequent tool for splitting long CRISPRs into shorter ones along a long evolutionary history.
authors.affiliation: Shenzhen Institutes of Advanced Technology and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.
authors.forename: Guoqin
authors.identifier: 0000-0003-1463-7152
authors.initials: G
authors.lastname: Mai
authors.affiliation: Shenzhen Institutes of Advanced Technology and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China; Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.
authors.forename: Ruiquan
authors.identifier: 0000-0001-7747-6937
authors.initials: R
authors.lastname: Ge
authors.affiliation: Shenzhen Institutes of Advanced Technology and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.
authors.forename: Guoquan
authors.initials: G
authors.lastname: Sun
authors.affiliation: Shenzhen Institutes of Advanced Technology and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China; Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.
authors.forename: Qinghan
authors.initials: Q
authors.lastname: Meng
authors.affiliation: College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China.
authors.forename: Fengfeng
authors.identifier: 0000-0002-8108-6007
authors.initials: F
authors.lastname: Zhou
mesh_terms: D064113:CRISPR-Cas Systems / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics; D066289:Data Curation / Q000379:methods*; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D011387:Prokaryotic Cells / Q000378:metabolism*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics
chemical_list: D021901:DNA, Intergenic