{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:43:29Z","timestamp":1767962609599,"version":"3.49.0"},"reference-count":35,"publisher":"Elsevier BV","issue":"3","license":[{"start":{"date-parts":[[2010,9,1]],"date-time":"2010-09-01T00:00:00Z","timestamp":1283299200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecular Phylogenetics and Evolution"],"published-print":{"date-parts":[[2010,9]]},"DOI":"10.1016\/j.ympev.2010.05.020","type":"journal-article","created":{"date-parts":[[2010,5,24]],"date-time":"2010-05-24T08:29:26Z","timestamp":1274689766000},"page":"878-887","source":"Crossref","is-referenced-by-count":55,"title":["Comparative network clustering of direct repeats (DRs) and cas genes confirms the possibility of the horizontal transfer of CRISPR locus among bacteria"],"prefix":"10.1016","volume":"56","author":[{"given":"Sajib","family":"Chakraborty","sequence":"first","affiliation":[]},{"given":"Ambrosius P.","family":"Snijders","sequence":"additional","affiliation":[]},{"given":"Rajib","family":"Chakravorty","sequence":"additional","affiliation":[]},{"given":"Musaddeque","family":"Ahmed","sequence":"additional","affiliation":[]},{"given":"Ashek Md.","family":"Tarek","sequence":"additional","affiliation":[]},{"given":"M. Anwar","family":"Hossain","sequence":"additional","affiliation":[]}],"member":"78","reference":[{"key":"10.1016\/j.ympev.2010.05.020_bib1","doi-asserted-by":"crossref","first-page":"1709","DOI":"10.1126\/science.1138140","article-title":"CRISPR provides acquired resistance against viruses in prokaryotes","volume":"315","author":"Barrangou","year":"2007","journal-title":"Science"},{"key":"10.1016\/j.ympev.2010.05.020_bib2","doi-asserted-by":"crossref","first-page":"2551","DOI":"10.1099\/mic.0.28048-0","article-title":"Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin","volume":"151","author":"Bolotin","year":"2005","journal-title":"Microbiology"},{"key":"10.1016\/j.ympev.2010.05.020_bib3","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1146\/annurev.genet.37.050503.084247","article-title":"Lateral gene transfer and the origins of prokaryotic groups","volume":"37","author":"Boucher","year":"2003","journal-title":"Annu. Rev. Genet."},{"key":"10.1016\/j.ympev.2010.05.020_bib4","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1126\/science.1159689","article-title":"Small CRISPR RNAs guide antiviral defense in prokaryotes","volume":"321","author":"Brouns","year":"2008","journal-title":"Science"},{"key":"10.1016\/j.ympev.2010.05.020_bib5","doi-asserted-by":"crossref","first-page":"1058","DOI":"10.1126\/science.273.5278.1058","article-title":"Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii","volume":"273","author":"Bult","year":"1996","journal-title":"Science"},{"key":"10.1016\/j.ympev.2010.05.020_bib6","doi-asserted-by":"crossref","first-page":"1390","DOI":"10.1128\/JB.01412-07","article-title":"Phage response to CRISPR-encoded resistance in Streptococcus thermophilus","volume":"190","author":"Deveau","year":"2008","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ympev.2010.05.020_bib7","doi-asserted-by":"crossref","first-page":"6106","DOI":"10.1128\/JB.187.17.6106-6118.2005","article-title":"Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: implications for phylogenetic inference and systematics","volume":"187","author":"Dewhirst","year":"2005","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ympev.2010.05.020_bib8","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1093\/bioinformatics\/17.9.853","article-title":"BioLayout \u2013 an automatic graph layout algorithm for similarity visualization","volume":"17","author":"Enright","year":"2001","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ympev.2010.05.020_bib9","first-page":"91","article-title":"Synonymous codon usage in bacteria","volume":"3","author":"Ermolaeva","year":"2001","journal-title":"Curr. Issues Mol. Biol."},{"key":"10.1016\/j.ympev.2010.05.020_bib10","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1007\/s00239-005-0223-z","article-title":"The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes","volume":"62","author":"Godde","year":"2006","journal-title":"J. Mol. Evol."},{"key":"10.1016\/j.ympev.2010.05.020_bib11","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/nrmicro1204","article-title":"Horizontal gene transfer, genome innovation and evolution","volume":"3","author":"Gogarten","year":"2005","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.ympev.2010.05.020_bib12","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1186\/1471-2105-8-172","article-title":"The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats","volume":"8","author":"Grissa","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.ympev.2010.05.020_bib13","doi-asserted-by":"crossref","first-page":"e60","DOI":"10.1371\/journal.pcbi.0010060","article-title":"A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR\/Cas subtypes exist in prokaryotic genomes","volume":"1","author":"Haft","year":"2005","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.ympev.2010.05.020_bib14","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1016\/j.cell.2009.07.040","article-title":"RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex","volume":"139","author":"Hale","year":"2009","journal-title":"Cell"},{"key":"10.1016\/j.ympev.2010.05.020_bib15","doi-asserted-by":"crossref","first-page":"5429","DOI":"10.1128\/jb.169.12.5429-5433.1987","article-title":"Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product","volume":"169","author":"Ishino","year":"1987","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ympev.2010.05.020_bib16","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1046\/j.1365-2958.2002.02839.x","article-title":"Identification of genes that are associated with DNA repeats in prokaryotes","volume":"43","author":"Jansen","year":"2002","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.ympev.2010.05.020_bib17","doi-asserted-by":"crossref","first-page":"e22","DOI":"10.1371\/journal.pgen.0030022","article-title":"Transition\u2013transversion bias is not universal: a counter example from grasshopper pseudogenes","volume":"3","author":"Keller","year":"2007","journal-title":"PLoS Genet."},{"key":"10.1016\/j.ympev.2010.05.020_bib18","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1146\/annurev.micro.55.1.709","article-title":"Horizontal gene transfer in prokaryotes: quantification and classification","volume":"55","author":"Koonin","year":"2001","journal-title":"Annu. Rev. Microbiol."},{"key":"10.1016\/j.ympev.2010.05.020_bib19","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1093\/bib\/bbn017","article-title":"MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences","volume":"9","author":"Kumar","year":"2008","journal-title":"Brief Bioinform."},{"key":"10.1016\/j.ympev.2010.05.020_bib20","doi-asserted-by":"crossref","first-page":"1843","DOI":"10.1093\/genetics\/143.4.1843","article-title":"Selfish operons: horizontal transfer may drive the evolution of gene clusters","volume":"143","author":"Lawrence","year":"1996","journal-title":"Genetics"},{"key":"10.1016\/j.ympev.2010.05.020_bib21","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1111\/j.1365-2958.2009.06641.x","article-title":"CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties","volume":"72","author":"Lillestol","year":"2009","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.ympev.2010.05.020_bib22","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1745-6150-1-7","article-title":"A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action","volume":"1","author":"Makarova","year":"2006","journal-title":"Biol. Direct"},{"key":"10.1016\/j.ympev.2010.05.020_bib23","doi-asserted-by":"crossref","first-page":"1843","DOI":"10.1126\/science.1165771","article-title":"CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA","volume":"322","author":"Marraffini","year":"2008","journal-title":"Science"},{"key":"10.1016\/j.ympev.2010.05.020_bib24","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1007\/s00239-004-0046-3","article-title":"Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements","volume":"60","author":"Mojica","year":"2005","journal-title":"J. Mol. Evol."},{"key":"10.1016\/j.ympev.2010.05.020_bib25","doi-asserted-by":"crossref","DOI":"10.1016\/j.ccm.2005.02.004","article-title":"The origin and evolution of Mycobacterium tuberculosis","volume":"26","author":"Mostowy","year":"2005","journal-title":"Clin. Chest Med."},{"key":"10.1016\/j.ympev.2010.05.020_bib26","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/20601","article-title":"Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima","volume":"399","author":"Nelson","year":"1999","journal-title":"Nature"},{"key":"10.1016\/j.ympev.2010.05.020_bib27","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1038\/35012500","article-title":"Lateral gene transfer and the nature of bacterial innovation","volume":"405","author":"Ochman","year":"2000","journal-title":"Nature"},{"key":"10.1016\/j.ympev.2010.05.020_bib28","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1007\/BF00166595","article-title":"Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory","volume":"40","author":"Ohta","year":"1995","journal-title":"J. Mol. Evol."},{"key":"10.1016\/j.ympev.2010.05.020_bib29","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1099\/mic.0.27437-0","article-title":"CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies","volume":"151","author":"Pourcel","year":"2005","journal-title":"Microbiology"},{"key":"10.1016\/j.ympev.2010.05.020_bib30","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1016\/S0959-437X(00)00244-6","article-title":"Detection of lateral gene transfer among microbial genomes","volume":"11","author":"Ragan","year":"2001","journal-title":"Curr. Opin. Genet. Dev."},{"key":"10.1016\/j.ympev.2010.05.020_bib31","first-page":"406","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"Saitou","year":"1987","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ympev.2010.05.020_bib32","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1042\/BST0370023","article-title":"Distribution of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism","volume":"37","author":"Shah","year":"2009","journal-title":"Biochem. Soc. Trans."},{"key":"10.1016\/j.ympev.2010.05.020_bib33","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1111\/j.1462-2920.2007.01444.x","article-title":"Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses","volume":"10","author":"Tyson","year":"2008","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.ympev.2010.05.020_bib34","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/j.tibs.2009.05.002","article-title":"CRISPR-based adaptive and heritable immunity in prokaryotes","volume":"34","author":"van der Oost","year":"2009","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/j.ympev.2010.05.020_bib35","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1093\/oxfordjournals.molbev.a026236","article-title":"Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models","volume":"17","author":"Yang","year":"2000","journal-title":"Mol. Biol. Evol."}],"container-title":["Molecular Phylogenetics and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1055790310002393?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1055790310002393?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,3,26]],"date-time":"2024-03-26T23:12:16Z","timestamp":1711494736000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1055790310002393"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,9]]},"references-count":35,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2010,9]]}},"alternative-id":["S1055790310002393"],"URL":"https:\/\/doi.org\/10.1016\/j.ympev.2010.05.020","relation":{},"ISSN":["1055-7903"],"issn-type":[{"value":"1055-7903","type":"print"}],"subject":[],"published":{"date-parts":[[2010,9]]}}}