{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T05:26:20Z","timestamp":1674624380391},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Establishment of intra-cellular life involved a profound re-configuration of the genetic characteristics of bacteria, including genome reduction and rearrangements. Understanding the mechanisms underlying these phenomena will shed light on the genome rearrangements essential for the development of an intra-cellular lifestyle. Comparison of genomes with differences in their sizes poses statistical as well as computational problems. Little efforts have been made to develop flexible computational tools with which to analyse genome reduction and rearrangements.<\/jats:p>\n               <jats:p>Results: Investigation of genome reduction and rearrangements in endosymbionts using a novel computational tool (GRAST) identified gathering of genes with similar functions. Conserved clusters of functionally related genes (CGSCs) were detected. Heterogeneous gene and gene cluster non-functionalization\/loss are identified between genome regions, functional gene categories and during evolution. Results show that gene non-functionalisation has accelerated during the last 50 MY of Buchnera's evolution while CGSCs have been static.<\/jats:p>\n               <jats:p>Availability: Software is available at<\/jats:p>\n               <jats:p>Contact: \u00a0mario.fares@nuim.ie<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl139","type":"journal-article","created":{"date-parts":[[2006,4,7]],"date-time":"2006-04-07T00:24:36Z","timestamp":1144369476000},"page":"1551-1561","source":"Crossref","is-referenced-by-count":2,"title":["GRAST: a new way of genome reduction analysis using comparative genomics"],"prefix":"10.1093","volume":"22","author":[{"given":"Christina","family":"Toft","sequence":"first","affiliation":[{"name":"Molecular Evolution and Bioinformatics Laboratory, Department of Biology, National University of Ireland \u00a0 Maynooth"}]},{"given":"Mario A.","family":"Fares","sequence":"additional","affiliation":[{"name":"Molecular Evolution and Bioinformatics Laboratory, Department of Biology, National University of Ireland \u00a0 Maynooth"}]}],"member":"286","published-online":{"date-parts":[[2006,4,6]]},"reference":[{"key":"2023012408340306800_b1","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1101\/gr.3844805","article-title":"The MicrobesOnline Web site for comparative genomics","volume":"15","author":"Alm","year":"2005","journal-title":"Genome Res."},{"key":"2023012408340306800_b2","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012408340306800_b3","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1093\/oxfordjournals.molbev.a026208","article-title":"Genome degradation is an ongoing process in Rickettsia","volume":"16","author":"Andersson","year":"1999","journal-title":"Mol. Biol. Evol."},{"key":"2023012408340306800_b4","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/S0966-842X(98)01312-2","article-title":"Reductive evolution of resident genomes","volume":"6","author":"Andersson","year":"1998","journal-title":"Trends Microbiol."},{"key":"2023012408340306800_b5","first-page":"0039","article-title":"KEGG-based pathway visualization tool for complex omics data","volume":"5","author":"Arakawa","year":"2005","journal-title":"In Silico Biol."},{"key":"2023012408340306800_b6","doi-asserted-by":"crossref","first-page":"1456","DOI":"10.1093\/molbev\/msi134","article-title":"Genome rearrangement distances and gene order phylogeny in gamma-Proteobacteria","volume":"22","author":"Belda","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"2023012408340306800_b7","doi-asserted-by":"crossref","first-page":"3422","DOI":"10.1093\/bioinformatics\/bti553","article-title":"ACT: the artemis comparison tool","volume":"21","author":"Carver","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012408340306800_b8","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1186\/1471-2105-5-52","article-title":"GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes","volume":"5","author":"Celamkoti","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023012408340306800_b9","doi-asserted-by":"crossref","first-page":"W734","DOI":"10.1093\/nar\/gki361","article-title":"The bioinformatics resource for oral pathogens","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012408340306800_b10","doi-asserted-by":"crossref","first-page":"2514","DOI":"10.1093\/bioinformatics\/bti350","article-title":"PLATCOM: a platform for computational comparative genomics","volume":"21","author":"Choi","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012408340306800_b11","doi-asserted-by":"crossref","first-page":"2307","DOI":"10.1093\/bioinformatics\/bth216","article-title":"GeConT: gene context analysis","volume":"20","author":"Ciria","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012408340306800_b12","doi-asserted-by":"crossref","first-page":"1162","DOI":"10.1093\/oxfordjournals.molbev.a004174","article-title":"The evolution of the heat-shock protein GroEL from Buchnera, the primary endosymbiont of aphids, is governed by positive selection","volume":"19","author":"Fares","year":"2002","journal-title":"Mol. Biol. Evol."},{"key":"2023012408340306800_b13","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1038\/417398a","article-title":"Endosymbiotic bacteria: groEL buffers against deleterious mutations","volume":"417","author":"Fares","year":"2002","journal-title":"Nature"},{"key":"2023012408340306800_b14","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1186\/1471-2105-5-198","article-title":"GenomeViz: visualizing microbial genomes","volume":"5","author":"Ghai","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023012408340306800_b15","doi-asserted-by":"crossref","first-page":"1449","DOI":"10.1093\/bioinformatics\/btg152","article-title":"Genome visualization made fast and simple","volume":"19","author":"Gibson","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012408340306800_b16","doi-asserted-by":"crossref","first-page":"4454","DOI":"10.1073\/pnas.062067299","article-title":"Extreme genome reduction in Buchnera spp.: toward the minimal genome needed for symbiotic life","volume":"99","author":"Gil","year":"2002","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012408340306800_b17","doi-asserted-by":"crossref","first-page":"2172","DOI":"10.1093\/molbev\/msh232","article-title":"The evolutionary fate of non-functional DNA in the bacterial endosymbiont Buchnera aphidicola","volume":"21","author":"Gomez-Valero","year":"2004","journal-title":"Mol. Biol. Evol."},{"key":"2023012408340306800_b18","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1038\/336435a0","article-title":"Deleterious mutations and the evolution of sexual reproduction","volume":"336","author":"Kondrashov","year":"1988","journal-title":"Nature"},{"key":"2023012408340306800_b19","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1093\/bioinformatics\/btg383","article-title":"BugView: a browser for comparing genomes","volume":"20","author":"Leader","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012408340306800_b20","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1093\/oxfordjournals.jhered.a111354","article-title":"The mutational meltdown in asexual populations","volume":"84","author":"Lynch","year":"1993","journal-title":"J. Hered"},{"key":"2023012408340306800_b21","doi-asserted-by":"crossref","first-page":"1268","DOI":"10.1038\/ng1470","article-title":"Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid","volume":"36","author":"McClelland","year":"2004","journal-title":"Nat. Genet."},{"key":"2023012408340306800_b22","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1016\/S0168-9525(01)02447-7","article-title":"Deletional bias and the evolution of bacterial genomes","volume":"17","author":"Mira","year":"2001","journal-title":"Trends Genet."},{"key":"2023012408340306800_b23","doi-asserted-by":"crossref","first-page":"2873","DOI":"10.1073\/pnas.93.7.2873","article-title":"Accelerated evolution and Muller's rachet in endosymbiotic bacteria","volume":"93","author":"Moran","year":"1996","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012408340306800_b24","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2001-2-12-research0054","article-title":"The process of genome shrinkage in the obligate symbiont Buchnera aphidicola","volume":"2","author":"Moran","year":"2001","journal-title":"Genome Biol."},{"key":"2023012408340306800_b25","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1093\/bioinformatics\/btk024","article-title":"BuchneraBASE: a post-genomic resource for Buchnera sp. APS","volume":"22","author":"Prickett","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012408340306800_b26","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1086\/303396","article-title":"Accumulation of deleterious mutations in endosymbionts: Muller's ratchet with two levels of selection","volume":"156","author":"Rispe","year":"2000","journal-title":"Am. Nat."},{"key":"2023012408340306800_b27","doi-asserted-by":"crossref","first-page":"3669","DOI":"10.1093\/bioinformatics\/bti606","article-title":"GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness","volume":"21","author":"Romualdi","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012408340306800_b28","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1007\/PL00006251","article-title":"Conserved gene clusters in bacterial genomes provide further support for the primacy of RNA","volume":"45","author":"Siefert","year":"1997","journal-title":"J. Mol. Evol."},{"key":"2023012408340306800_b29","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1016\/S0168-9525(01)02483-0","article-title":"Genome size reduction through multiple events of gene disintegration in Buchnera APS","volume":"17","author":"Silva","year":"2001","journal-title":"Trends Genet."},{"key":"2023012408340306800_b30","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/S0168-9525(03)00041-6","article-title":"Why are the genomes of endosymbiotic bacteria so stable?","volume":"19","author":"Silva","year":"2003","journal-title":"Trends Genet."},{"key":"2023012408340306800_b31","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1093\/bioinformatics\/bti054","article-title":"Circular genome visualization and exploration using CGView","volume":"21","author":"Stothard","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012408340306800_b32","doi-asserted-by":"crossref","first-page":"2376","DOI":"10.1126\/science.1071278","article-title":"50 million years of genomic stasis in endosymbiotic bacteria","volume":"296","author":"Tamas","year":"2002","journal-title":"Science"},{"key":"2023012408340306800_b33","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1471-2105-4-41","article-title":"The COG database: an updated version includes eukaryotes","volume":"4","author":"Tatusov","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"2023012408340306800_b34","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1126\/science.278.5338.631","article-title":"A genomic perspective on protein families","volume":"278","author":"Tatusov","year":"1997","journal-title":"Science"},{"key":"2023012408340306800_b35","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1186\/1471-2105-4-53","article-title":"GeneViTo: visualizing gene-product functional and structural features in genomic datasets","volume":"4","author":"Vernikos","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"2023012408340306800_b36","doi-asserted-by":"crossref","first-page":"D433","DOI":"10.1093\/nar\/gki005","article-title":"STRING: known and predicted protein\u2013protein associations, integrated and transferred across organisms","volume":"33","author":"von Mering","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012408340306800_b37","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1093\/bioinformatics\/btg121","article-title":"ACGT-a comparative genomics tool","volume":"19","author":"Xie","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012408340306800_b38","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1016\/S0167-7012(03)00094-0","article-title":"GenomeComp: a visualization tool for microbial genome comparison","volume":"54","author":"Yang","year":"2003","journal-title":"J. Microbiol. Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/13\/1551\/48839248\/bioinformatics_22_13_1551.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/13\/1551\/48839248\/bioinformatics_22_13_1551.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T08:52:45Z","timestamp":1674550365000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/13\/1551\/193590"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,4,6]]},"references-count":38,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2006,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl139","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,7,1]]},"published":{"date-parts":[[2006,4,6]]}}}