{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T04:03:05Z","timestamp":1778126585791,"version":"3.51.4"},"reference-count":95,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,3]]},"DOI":"10.1093\/gbe\/evt027","type":"journal-article","created":{"date-parts":[[2013,2,22]],"date-time":"2013-02-22T01:17:06Z","timestamp":1361495826000},"page":"542-558","source":"Crossref","is-referenced-by-count":111,"title":["Replicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti"],"prefix":"10.1093","volume":"5","author":[{"given":"Marco","family":"Galardini","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesco","family":"Pini","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Bazzicalupo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emanuele G.","family":"Biondi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessio","family":"Mengoni","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,2,21]]},"reference":[{"key":"key\n\t\t\t\t20170627101306_evt027-B1","doi-asserted-by":"crossref","first-page":"e9","DOI":"10.1093\/bioinformatics\/btl213","article-title":"Automatic clustering of orthologs and inparalogs shared by multiple proteomes","volume":"22","author":"Alexeyenko","year":"2006","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B2","doi-asserted-by":"crossref","first-page":"e1000262","DOI":"10.1371\/journal.pcbi.1000262","article-title":"Phylogenetic and functional assessment of orthologs inference projects and methods","volume":"5","author":"Altenhoff","year":"2009","journal-title":"PLoS Comput Biol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B3","doi-asserted-by":"crossref","first-page":"2719","DOI":"10.1111\/j.1365-294X.2006.02969.x","article-title":"Recombination and selection shape the molecular diversity pattern of nitrogen-fixing Sinorhizobium sp","volume":"15","author":"Bailly","year":"2006","journal-title":"associated to Medicago. Mol Ecol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B4","doi-asserted-by":"crossref","first-page":"1722","DOI":"10.1038\/ismej.2011.55","article-title":"Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates","volume":"5","author":"Bailly","year":"2011","journal-title":"ISME J."},{"key":"key\n\t\t\t\t20170627101306_evt027-B5","doi-asserted-by":"crossref","first-page":"2255","DOI":"10.1128\/JB.01666-09","article-title":"Dual control of Sinorhizobium meliloti RpoE2 sigma factor activity by Two PhyR-type two-component response regulators","volume":"192","author":"Bastiat","year":"2010","journal-title":"J Bacteriol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B6","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1517\/14622416.5.4.433","article-title":"Solexa Ltd","volume":"5","author":"Bennett","year":"2004","journal-title":"Pharmacogenomics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B7","first-page":"188","article-title":"R factor transfer in Rhizobium leguminosarum","volume":"84","author":"Beringer","year":"1974","journal-title":"J Gen Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B8","doi-asserted-by":"crossref","first-page":"2","DOI":"10.4161\/mge.1.1.15316","article-title":"Spread of the group II intron RmInt1 and its insertion sequence target sites in the plant endosymbiont Sinorhizobium meliloti","volume":"1","author":"Biondi","year":"2011","journal-title":"Mob Genet Elements."},{"key":"key\n\t\t\t\t20170627101306_evt027-B9","doi-asserted-by":"crossref","first-page":"5396","DOI":"10.1128\/AEM.00196-09","article-title":"Metabolic capacity of Sinorhizobium (Ensifer) meliloti strains as determined by phenotype microarray analysis","volume":"75","author":"Biondi","year":"2009","journal-title":"Appl Environ Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B10","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/j.tig.2006.06.005","article-title":"Genomic insights into positive selection","volume":"22","author":"Biswas","year":"2006","journal-title":"Trends Genet."},{"key":"key\n\t\t\t\t20170627101306_evt027-B11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v007.i10","article-title":"zt: a software tool for simple and partial Mantel tests","volume":"7","author":"Bonnet","year":"2002","journal-title":"J Stat Software."},{"key":"key\n\t\t\t\t20170627101306_evt027-B12","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1098\/rspb.2009.1679","article-title":"Horizontal gene transfer in evolution: facts and challenges","volume":"277","author":"Boto","year":"2010","journal-title":"Proc Biol Sci."},{"key":"key\n\t\t\t\t20170627101306_evt027-B13","doi-asserted-by":"crossref","first-page":"67","DOI":"10.4137\/EBO.S2242","article-title":"A mixture model and a hidden Markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies","volume":"5","author":"Boussau","year":"2009","journal-title":"Evol Bioinform Online."},{"key":"key\n\t\t\t\t20170627101306_evt027-B14","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1016\/S0966-842X(01)02131-X","article-title":"The evolution of mycobacterial pathogenicity: clues from comparative genomics","volume":"9","author":"Brosch","year":"2001","journal-title":"Trends Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B15","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B16","doi-asserted-by":"crossref","first-page":"4785","DOI":"10.1128\/AEM.66.11.4785-4789.2000","article-title":"Genetic diversity and dynamics of Sinorhizobium meliloti populations nodulating different alfalfa varieties in Italian soils","volume":"66","author":"Carelli","year":"2000","journal-title":"Appl Environ Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B17","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1038\/nature11184","article-title":"Proto-genes and de novo gene birth","volume":"487","author":"Carvunis","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170627101306_evt027-B18","doi-asserted-by":"crossref","first-page":"7271","DOI":"10.1128\/AEM.71.11.7271-7278.2005","article-title":"Ascending migration of endophytic rhizobia, from roots to leaves, inside rice plants and assessment of benefits to rice growth physiology","volume":"71","author":"Chi","year":"2005","journal-title":"Appl Environ Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B19","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.mib.2010.08.007","article-title":"Genomic evolution of Vibrio cholerae","volume":"13","author":"Cho","year":"2010","journal-title":"Curr Opin Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B20","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B21","doi-asserted-by":"crossref","first-page":"3674","DOI":"10.1093\/bioinformatics\/bti610","article-title":"Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research","volume":"21","author":"Conesa","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B22","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: multiple alignment of conserved genomic sequence with rearrangements","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170627101306_evt027-B23","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi1104s17","article-title":"Assembling genomic DNA sequences with PHRAP","author":"de la Bastide","year":"2007","journal-title":"Curr Protoc Bioinformatics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B24","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1186\/1471-2164-11-500","article-title":"Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification","volume":"11","author":"Deng","year":"2010","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B25","doi-asserted-by":"crossref","first-page":"2330","DOI":"10.1128\/JB.185.7.2330-2337.2003","article-title":"Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18","volume":"185","author":"Deng","year":"2003","journal-title":"J Bacteriol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B26","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1093\/molbev\/msr317","article-title":"Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis","volume":"29","author":"de Vienne","year":"2012","journal-title":"Mol Biol Evol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B27","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1186\/gb-2006-7-9-116","article-title":"Genomics and the bacterial species problem","volume":"7","author":"Doolittle","year":"2006","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B28","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-5-113","article-title":"MUSCLE: a multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"Edgar","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B29","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1016\/S0966-842X(01)02293-4","article-title":"Comparative genomics of closely related salmonellae","volume":"10","author":"Edwards","year":"2002","journal-title":"Trends Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B30","doi-asserted-by":"crossref","first-page":"e1002868","DOI":"10.1371\/journal.pgen.1002868","article-title":"Population genomics of the facultatively mutualistic bacteria Sinorhizobium meliloti and S. medicae","volume":"8","author":"Epstein","year":"2012","journal-title":"PLoS Genet."},{"key":"key\n\t\t\t\t20170627101306_evt027-B31","doi-asserted-by":"crossref","first-page":"9889","DOI":"10.1073\/pnas.161294698","article-title":"The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti","volume":"98","author":"Finan","year":"2001","journal-title":"Proc Natl Acad Sci U S A."},{"key":"key\n\t\t\t\t20170627101306_evt027-B32","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1186\/1471-2180-10-65","article-title":"Comparative genomics of VirR regulons in Clostridium perfringens strains","volume":"10","author":"Frandi","year":"2010","journal-title":"BMC Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B33","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1751-0473-6-11","article-title":"CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes","volume":"6","author":"Galardini","year":"2011","journal-title":"Source Code Biol Med."},{"key":"key\n\t\t\t\t20170627101306_evt027-B34","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1186\/1471-2164-12-235","article-title":"Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti","volume":"12","author":"Galardini","year":"2011","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B35","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1126\/science.1060966","article-title":"The composite genome of the legume symbiont Sinorhizobium meliloti","volume":"293","author":"Galibert","year":"2001","journal-title":"Science"},{"key":"key\n\t\t\t\t20170627101306_evt027-B36","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1146\/annurev.genet.42.110807.091427","article-title":"Molecular determinants of a symbiotic chronic infection","volume":"42","author":"Gibson","year":"2008","journal-title":"Annu Rev Genet."},{"key":"key\n\t\t\t\t20170627101306_evt027-B37","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1186\/1471-2164-6-158","article-title":"Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains","volume":"6","author":"Giuntini","year":"2005","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B38","doi-asserted-by":"crossref","first-page":"1485","DOI":"10.1101\/gad.7.8.1485","article-title":"A Rhizobium meliloti homolog of the Escherichia coli peptide-antibiotic transport protein SbmA is essential for bacteroid development","volume":"7","author":"Glazebrook","year":"1993","journal-title":"Genes Dev."},{"key":"key\n\t\t\t\t20170627101306_evt027-B39","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":"key\n\t\t\t\t20170627101306_evt027-B40","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1139\/G09-060","article-title":"Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti","volume":"52","author":"Guo","year":"2009","journal-title":"Genome"},{"key":"key\n\t\t\t\t20170627101306_evt027-B41","first-page":"9","article-title":"PAST: Paleontological Statistics Software Package for education and data analysis","volume":"41","author":"Hammer","year":"2001","journal-title":"Palaeontol Electron."},{"key":"key\n\t\t\t\t20170627101306_evt027-B42","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.tim.2009.12.010","article-title":"Introducing the bacterial \u201cchromid\u201d: not a chromosome, not a plasmid","volume":"18","author":"Harrison","year":"2010","journal-title":"Trends Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B43","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1093\/bioinformatics\/17.8.754","article-title":"MRBAYES: Bayesian inference of phylogenetic trees","volume":"17","author":"Huelsenbeck","year":"2001","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B44","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B45","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1094\/MPMI-21-7-0979","article-title":"Mutational analysis of the Sinorhizobium meliloti short-chain dehydrogenase\/reductase family reveals substantial contribution to symbiosis and catabolic diversity","volume":"21","author":"Jacob","year":"2008","journal-title":"Mol Plant Microbe Interact."},{"key":"key\n\t\t\t\t20170627101306_evt027-B46","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1139\/w00-135","article-title":"Genetic diversity of Sinorhizobium populations recovered from different Medicago varieties cultivated in Tunisian soils","volume":"47","author":"Jebara","year":"2001","journal-title":"Can J Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B47","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1128\/JB.187.4.1293-1304.2005","article-title":"Ectoine-induced proteins in Sinorhizobium meliloti include an ectoine ABC-type transporter involved in osmoprotection and ectoine catabolism","volume":"187","author":"Jebbar","year":"2005","journal-title":"J Bacteriol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B48","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1186\/1471-2164-12-32","article-title":"Genomic fluidity: an integrative view of gene diversity within microbial populations","volume":"12","author":"Kislyuk","year":"2011","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B49","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1093\/nar\/gkp089","article-title":"Darwinian evolution in the light of genomics","volume":"37","author":"Koonin","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170627101306_evt027-B50","doi-asserted-by":"crossref","first-page":"e1002173","DOI":"10.1371\/journal.pcbi.1002173","article-title":"Are there laws of genome evolution?","volume":"7","author":"Koonin","year":"2011","journal-title":"PLoS Comput Biol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B51","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1038\/nrg2810","article-title":"Constraints and plasticity in genome and molecular-phenome evolution","volume":"11","author":"Koonin","year":"2010","journal-title":"Nat Rev Genet."},{"key":"key\n\t\t\t\t20170627101306_evt027-B52","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1128\/MMBR.54.4.502-539.1990","article-title":"Organization of the bacterial chromosome","volume":"54","author":"Krawiec","year":"1990","journal-title":"Microbiol Rev."},{"key":"key\n\t\t\t\t20170627101306_evt027-B53","doi-asserted-by":"crossref","first-page":"1450","DOI":"10.1101\/gr.091785.109","article-title":"The consequences of genetic drift for bacterial genome complexity","volume":"19","author":"Kuo","year":"2009","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170627101306_evt027-B54","doi-asserted-by":"crossref","first-page":"3100","DOI":"10.1093\/nar\/gkm160","article-title":"RNAmmer: consistent and rapid annotation of ribosomal RNA genes","volume":"35","author":"Lagesen","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170627101306_evt027-B55","doi-asserted-by":"crossref","first-page":"R71","DOI":"10.1186\/gb-2007-8-5-r71","article-title":"Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition","volume":"8","author":"Lefebure","year":"2007","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B56","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.0955","article-title":"TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence","volume":"25","author":"Lowe","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170627101306_evt027-B57","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1007\/s00248-010-9717-3","article-title":"Comparison of 61 sequenced Escherichia coli genomes","volume":"60","author":"Lukjancenko","year":"2010","journal-title":"Microb Ecol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B58","doi-asserted-by":"crossref","first-page":"1753","DOI":"10.1534\/genetics.104.032144","article-title":"Detecting amino acid sites under positive selection and purifying selection","volume":"169","author":"Massingham","year":"2005","journal-title":"Genetics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B59","article-title":"Gephi: an open source software for exploring and manipulating networks","volume-title":"International AAAI Conference on Weblogs and Social Media","author":"Mathieu","year":"2009"},{"key":"key\n\t\t\t\t20170627101306_evt027-B60","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1128\/JB.149.1.114-122.1982","article-title":"Physical and genetic characterization of symbiotic and auxotrophic mutants of Rhizobium meliloti induced by transposon Tn5 mutagenesis","volume":"149","author":"Meade","year":"1982","journal-title":"J Bacteriol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B61","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1038\/nrmicro1901","article-title":"Microbiology in the post-genomic era","volume":"6","author":"Medini","year":"2008","journal-title":"Nat Rev Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B62","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1093\/bioinformatics\/btp666","article-title":"Tablet\u2014next generation sequence assembly visualization","volume":"26","author":"Milne","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B63","doi-asserted-by":"crossref","first-page":"2933","DOI":"10.1111\/j.1462-2920.2007.01404.x","article-title":"Metabolic capacity of Bacillus cereus strains ATCC 14579 and ATCC 10987 interlinked with comparative genomics","volume":"9","author":"Mols","year":"2007","journal-title":"Environ Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B64","doi-asserted-by":"crossref","first-page":"W182","DOI":"10.1093\/nar\/gkm321","article-title":"KAAS: an automatic genome annotation and pathway reconstruction server","volume":"35","author":"Moriya","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170627101306_evt027-B65","doi-asserted-by":"crossref","first-page":"D476","DOI":"10.1093\/nar\/gki107","article-title":"Inparanoid: a comprehensive database of eukaryotic orthologs","volume":"33","author":"O'Brien","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170627101306_evt027-B66","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1186\/1471-2105-12-385","article-title":"Interactive metagenomic visualization in a Web browser","volume":"12","author":"Ondov","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B67","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1023\/A:1000591719287","article-title":"Influence of plant genotype on the selection of nodulating Sinorhizobium meliloti strains by Medicago sativa","volume":"73","author":"Paffetti","year":"1998","journal-title":"Antonie Van Leeuwenhoek"},{"key":"key\n\t\t\t\t20170627101306_evt027-B68","doi-asserted-by":"crossref","first-page":"2279","DOI":"10.1128\/AEM.62.7.2279-2285.1996","article-title":"Genetic diversity of an Italian Rhizobium meliloti population from different Medicago sativa varieties","volume":"62","author":"Paffetti","year":"1996","journal-title":"Appl Environ Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B69","first-page":"357","article-title":"TreeView: an application to display phylogenetic trees on personal computers","volume":"12","author":"Page","year":"1996","journal-title":"Comput Appl Biosci."},{"key":"key\n\t\t\t\t20170627101306_evt027-B70","first-page":"2825","article-title":"Scikit-learn: machine learning in Python","volume":"12","author":"Pedregosa","year":"2011","journal-title":"J Machine Learning Res."},{"key":"key\n\t\t\t\t20170627101306_evt027-B71","doi-asserted-by":"crossref","first-page":"1336","DOI":"10.1101\/gr.6254707","article-title":"Genes under positive selection in Escherichia coli","volume":"17","author":"Petersen","year":"2007","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170627101306_evt027-B72","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/1471-2180-12-78","article-title":"Exploring the plant-associated bacterial communities in Medicago sativa L","volume":"12","author":"Pini","year":"2012","journal-title":"BMC Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B73","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.3390\/genes2041017","article-title":"Plant-bacteria association and symbiosis: are there common genomic traits in Alphaproteobacteria?","volume":"2","author":"Pini","year":"2011","journal-title":"Genes"},{"key":"key\n\t\t\t\t20170627101306_evt027-B74","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1101\/gr.115592.110","article-title":"Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes","volume":"21","author":"Popa","year":"2011","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170627101306_evt027-B75","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1093\/bioinformatics\/btk021","article-title":"GenomeDiagram: a python package for the visualization of large-scale genomic data","volume":"22","author":"Pritchard","year":"2006","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B76","doi-asserted-by":"crossref","first-page":"6881","DOI":"10.1128\/JB.00619-08","article-title":"The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates","volume":"190","author":"Rasko","year":"2008","journal-title":"J Bacteriol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B77","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1006\/jmbi.2000.5197","article-title":"Automatic clustering of orthologs and in-paralogs from pairwise species comparisons","volume":"314","author":"Remm","year":"2001","journal-title":"J Mol Biol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B78","doi-asserted-by":"crossref","first-page":"15305","DOI":"10.1073\/pnas.93.26.15305","article-title":"The common nodABC genes of Rhizobium meliloti are host-range determinants","volume":"93","author":"Roche","year":"1996","journal-title":"Proc Natl Acad Sci U S A."},{"key":"key\n\t\t\t\t20170627101306_evt027-B79","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1007\/BF00279746","article-title":"Molecular and genetic characterization of the rhizopine catabolism (mocABRC) genes of Rhizobium meliloti L5\u201330","volume":"245","author":"Rossbach","year":"1994","journal-title":"Mol Gen Genet."},{"key":"key\n\t\t\t\t20170627101306_evt027-B80","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.jbiotec.2010.12.018","article-title":"The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome","volume":"155","author":"Schneiker-Bekel","year":"2011","journal-title":"J Biotechnol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B81","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1101\/gr.089532.108","article-title":"ABySS: a parallel assembler for short read sequence data","volume":"19","author":"Simpson","year":"2009","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170627101306_evt027-B82","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1186\/1471-2148-9-264","article-title":"Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes","volume":"9","author":"Soyer","year":"2009","journal-title":"BMC Evol Biol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B83","volume-title":"Nodulation in legumes","author":"Sprent","year":"2001"},{"key":"key\n\t\t\t\t20170627101306_evt027-B84","doi-asserted-by":"crossref","first-page":"1569","DOI":"10.1093\/bioinformatics\/btq228","article-title":"DendroPy: a Python library for phylogenetic computing","volume":"26","author":"Sukumaran","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B85","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1111\/j.1574-6968.2008.01329.x","article-title":"Diversity of Sinorhizobium strains nodulating Medicago sativa from different Iranian regions","volume":"288","author":"Talebi Bedaf","year":"2008","journal-title":"FEMS Microbiol Lett."},{"key":"key\n\t\t\t\t20170627101306_evt027-B86","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1093\/molbev\/msr121","article-title":"MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods","volume":"28","author":"Tamura","year":"2011","journal-title":"Mol Biol Evol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B87","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1093\/nar\/29.1.22","article-title":"The COG database: new developments in phylogenetic classification of proteins from complete genomes","volume":"29","author":"Tatusov","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170627101306_evt027-B88","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1016\/j.mib.2008.09.006","article-title":"Comparative genomics: the bacterial pan-genome","volume":"11","author":"Tettelin","year":"2008","journal-title":"Curr Opin Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B89","doi-asserted-by":"crossref","first-page":"8629","DOI":"10.1073\/pnas.1120436109","article-title":"Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations","volume":"109","author":"Tian","year":"2012","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"3","key":"key\n\t\t\t\t20170627101306_evt027-B90","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1007\/s13213-010-0084-6","article-title":"Genetic diversity and salt tolerance of Sinorhizobium populations from two Tunisian soils","volume":"60","author":"Trabelsi","year":"2010","journal-title":"Ann Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B91","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1111\/j.1472-765X.2008.02532.x","article-title":"Development of real-time PCR assay for detection and quantification of Sinorhizobium meliloti in soil and plant tissue","volume":"48","author":"Trabelsi","year":"2009","journal-title":"Lett Appl Microbiol."},{"key":"key\n\t\t\t\t20170627101306_evt027-B92","first-page":"555","article-title":"PAML: a program package for phylogenetic analysis by maximum likelihood","volume":"13","author":"Yang","year":"1997","journal-title":"Comput Appl Biosci."},{"key":"key\n\t\t\t\t20170627101306_evt027-B93","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1093\/bioinformatics\/btq093","article-title":"Composition bias and the origin of ORFan genes","volume":"26","author":"Yomtovian","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B94","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1093\/bioinformatics\/17.9.847","article-title":"InterProScan\u2014an integration platform for the signature-recognition methods in InterPro","volume":"17","author":"Zdobnov","year":"2001","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170627101306_evt027-B95","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1534\/genetics.106.061432","article-title":"Statistical tests for detecting positive selection by utilizing high-frequency variants","volume":"174","author":"Zeng","year":"2006","journal-title":"Genetics"}],"container-title":["Genome Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/gbe\/article-pdf\/5\/3\/542\/17919643\/evt027.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,7,22]],"date-time":"2020-07-22T17:59:42Z","timestamp":1595440782000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gbe\/article-lookup\/doi\/10.1093\/gbe\/evt027"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,2,21]]},"references-count":95,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2013,2,21]]},"published-print":{"date-parts":[[2013,3]]}},"URL":"https:\/\/doi.org\/10.1093\/gbe\/evt027","relation":{},"ISSN":["1759-6653"],"issn-type":[{"value":"1759-6653","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,2,21]]}}}