메뉴 건너뛰기




Volumn 5, Issue 3, 2013, Pages 542-558

Replicon-dependent bacterial genome evolution: The case of Sinorhizobium meliloti

Author keywords

Bacteria; Chromid; Pangenome; Selection

Indexed keywords

BACTERIA (MICROORGANISMS); SINORHIZOBIUM MELILOTI;

EID: 84876520217     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evt027     Document Type: Article
Times cited : (83)

References (95)
  • 1
    • 33747892409 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and inparalogs shared by multiple proteomes
    • Alexeyenko A, Tamas I, Liu G, Sonnhammer ELL. 2006. Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 22:e9-e15.
    • (2006) Bioinformatics , vol.22
    • Alexeyenko, A.1    Tamas, I.2    Liu, G.3    Sonnhammer, E.L.L.4
  • 2
    • 59149102602 scopus 로고    scopus 로고
    • Phylogenetic and functional assessment of orthologs inference projects and methods
    • Altenhoff AM, Dessimoz C. 2009. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol. 5: e1000262.
    • (2009) PLoS Comput Biol. , vol.5
    • Altenhoff, A.M.1    Dessimoz, C.2
  • 3
    • 33747060705 scopus 로고    scopus 로고
    • Recombination and selection shape the molecular diversity pattern of nitrogen-fixing Sinorhizobium sp. associated to Medicago
    • Bailly X, Olivieri I, De Mita S, Cleyet-Marel JC, Bena G. 2006. Recombination and selection shape the molecular diversity pattern of nitrogen-fixing Sinorhizobium sp. associated to Medicago. Mol Ecol. 15:2719-2734.
    • (2006) Mol Ecol. , vol.15 , pp. 2719-2734
    • Bailly, X.1    Olivieri, I.2    De Mita, S.3    Cleyet-Marel, J.C.4    Bena, G.5
  • 4
    • 80054765048 scopus 로고    scopus 로고
    • Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates
    • Bailly X, et al. 2011. Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates. ISME J. 5: 1722-1734.
    • (2011) ISME J. , vol.5 , pp. 1722-1734
    • Bailly, X.1
  • 5
    • 77950651423 scopus 로고    scopus 로고
    • Dual control of Sinorhizobium meliloti RpoE2 sigma factor activity by Two PhyR-type two-component response regulators
    • Bastiat BND, Sauviac L, Bruand C. 2010. Dual control of Sinorhizobium meliloti RpoE2 sigma factor activity by Two PhyR-type two-component response regulators. J Bacteriol. 192:2255-2265.
    • (2010) J Bacteriol. , vol.192 , pp. 2255-2265
    • Bastiat, B.N.D.1    Sauviac, L.2    Bruand, C.3
  • 7
    • 0016231913 scopus 로고
    • R factor transfer in Rhizobium leguminosarum
    • Beringer JE. 1974. R factor transfer in Rhizobium leguminosarum. J Gen Microbiol. 84:188-198.
    • (1974) J Gen Microbiol. , vol.84 , pp. 188-198
    • Beringer, J.E.1
  • 8
    • 84871339426 scopus 로고    scopus 로고
    • Spread of the group II intron RmInt1 and its insertion sequence target sites in the plant endosymbiont Sinorhizobium meliloti
    • Biondi EG, Toro NS, Bazzicalupo M, Martinez-Abarca F. 2011. Spread of the group II intron RmInt1 and its insertion sequence target sites in the plant endosymbiont Sinorhizobium meliloti. Mob Genet Elements. 1: 2-7.
    • (2011) Mob Genet Elements. , vol.1 , pp. 2-7
    • Biondi, E.G.1    Toro, N.S.2    Bazzicalupo, M.3    Martinez-Abarca, F.4
  • 9
    • 68549122764 scopus 로고    scopus 로고
    • Metabolic capacity of Sinorhizobium (Ensifer) meliloti strains as determined by phenotype microarray analysis
    • Biondi EG, et al. 2009. Metabolic capacity of Sinorhizobium (Ensifer) meliloti strains as determined by phenotype microarray analysis. Appl Environ Microbiol. 75:5396-5404.
    • (2009) Appl Environ Microbiol. , vol.75 , pp. 5396-5404
    • Biondi, E.G.1
  • 10
    • 33746237567 scopus 로고    scopus 로고
    • Genomic insights into positive selection
    • Biswas S, Akey JM. 2006. Genomic insights into positive selection. Trends Genet. 22:437-446.
    • (2006) Trends Genet. , vol.22 , pp. 437-446
    • Biswas, S.1    Akey, J.M.2
  • 11
    • 1542364165 scopus 로고    scopus 로고
    • Zt: A software tool for simple and partial Mantel tests
    • Bonnet E, Van de Peer Y. 2002. zt: a software tool for simple and partial Mantel tests. J Stat Software. 7:1-12.
    • (2002) J Stat Software , vol.7 , pp. 1-12
    • Bonnet, E.1    Van De Peer, Y.2
  • 12
    • 77950195231 scopus 로고    scopus 로고
    • Horizontal gene transfer in evolution: Facts and challenges
    • Boto L. 2010. Horizontal gene transfer in evolution: facts and challenges. Proc Biol Sci. 277:819-827.
    • (2010) Proc Biol Sci. , vol.277 , pp. 819-827
    • Boto, L.1
  • 13
    • 68149165460 scopus 로고    scopus 로고
    • A mixture model and a hidden Markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies
    • Boussau B, Gueguen L, Gouy M. 2009. A mixture model and a hidden Markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies. Evol Bioinform Online. 5: 67-79.
    • (2009) Evol Bioinform Online , vol.5 , pp. 67-79
    • Boussau, B.1    Gueguen, L.2    Gouy, M.3
  • 14
    • 0035448545 scopus 로고    scopus 로고
    • The evolution of mycobacterial pathogenicity: Clues from comparative genomics
    • Brosch R, Pym AS, Gordon SV, Cole ST. 2001. The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol. 9:452-458.
    • (2001) Trends Microbiol. , vol.9 , pp. 452-458
    • Brosch, R.1    Pym, A.S.2    Gordon, S.V.3    Cole, S.T.4
  • 15
    • 74049108922 scopus 로고    scopus 로고
    • BLAST+: Architecture and applications
    • Camacho C, et al. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10:421.
    • (2009) BMC Bioinformatics , vol.10 , pp. 421
    • Camacho, C.1
  • 16
    • 0033754493 scopus 로고    scopus 로고
    • Genetic diversity and dynamics of Sinorhizobium meliloti populations nodulating different alfalfa varieties in Italian soils
    • Carelli M, et al. 2000. Genetic diversity and dynamics of Sinorhizobium meliloti populations nodulating different alfalfa varieties in Italian soils. Appl Environ Microbiol. 66:4785-4789.
    • (2000) Appl Environ Microbiol. , vol.66 , pp. 4785-4789
    • Carelli, M.1
  • 17
    • 84863988094 scopus 로고    scopus 로고
    • Proto-genes and de novo gene birth
    • Carvunis A-R, et al. 2012. Proto-genes and de novo gene birth. Nature 487:370-374.
    • (2012) Nature , vol.487 , pp. 370-374
    • Carvunis, A.-R.1
  • 18
    • 32044473489 scopus 로고    scopus 로고
    • Ascending migration of endophytic rhizobia, from roots to leaves, inside rice plants and assessment of benefits to rice growth physiology
    • Chi F, et al. 2005. Ascending migration of endophytic rhizobia, from roots to leaves, inside rice plants and assessment of benefits to rice growth physiology. Appl Environ Microbiol. 71:7271-7278.
    • (2005) Appl Environ Microbiol. , vol.71 , pp. 7271-7278
    • Chi, F.1
  • 20
    • 65649092976 scopus 로고    scopus 로고
    • Biopython: Freely available Python tools for computational molecular biology and bioinformatics
    • Cock PJ, et al. 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422-1423.
    • (2009) Bioinformatics , vol.25 , pp. 1422-1423
    • Cock, P.J.1
  • 21
    • 24644503098 scopus 로고    scopus 로고
    • Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research
    • Conesa A, et al. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
    • (2005) Bioinformatics , vol.21 , pp. 3674-3676
    • Conesa, A.1
  • 22
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: Multiple alignment of conserved genomic sequence with rearrangements
    • Darling AC, Mau B, Blattner FR, Perna NT. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14:1394-1403.
    • (2004) Genome Res. , vol.14 , pp. 1394-1403
    • Darling, A.C.1    Mau, B.2    Blattner, F.R.3    Perna, N.T.4
  • 24
    • 77956600970 scopus 로고    scopus 로고
    • Probing the pan-genome of Listeria monocytogenes: New insights into intraspecific niche expansion and genomic diversification
    • Deng X, Phillippy AM, Li Z, Salzberg SL, Zhang W. 2010. Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification. BMC Genomics 11:500.
    • (2010) BMC Genomics , vol.11 , pp. 500
    • Deng, X.1    Phillippy, A.M.2    Li, Z.3    Salzberg, S.L.4    Zhang, W.5
  • 25
    • 0037377818 scopus 로고    scopus 로고
    • Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18
    • Deng W, et al. 2003. Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J Bacteriol. 185:2330-2337.
    • (2003) J Bacteriol. , vol.185 , pp. 2330-2337
    • Deng, W.1
  • 26
    • 84861368644 scopus 로고    scopus 로고
    • Phylo-MCOA: A fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis
    • de Vienne DM, Ollier S, Aguileta G. 2012. Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis. Mol Biol Evol. 29:1587-1598.
    • (2012) Mol Biol Evol. , vol.29 , pp. 1587-1598
    • De Vienne, D.M.1    Ollier, S.2    Aguileta, G.3
  • 27
    • 33845890829 scopus 로고    scopus 로고
    • Genomics and the bacterial species problem
    • Doolittle WF, Papke RT. 2006. Genomics and the bacterial species problem. Genome Biol. 7:116.
    • (2006) Genome Biol. , vol.7 , pp. 116
    • Doolittle, W.F.1    Papke, R.T.2
  • 28
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113.
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 29
    • 0036468520 scopus 로고    scopus 로고
    • Comparative genomics of closely related salmonellae
    • Edwards RA, Olsen GJ, Maloy SR. 2002. Comparative genomics of closely related salmonellae. Trends Microbiol. 10:94-99.
    • (2002) Trends Microbiol. , vol.10 , pp. 94-99
    • Edwards, R.A.1    Olsen, G.J.2    Maloy, S.R.3
  • 30
    • 84866148788 scopus 로고    scopus 로고
    • Population genomics of the facultatively mutualistic bacteria Sinorhizobium meliloti and S. medicae
    • Epstein B, et al. 2012. Population genomics of the facultatively mutualistic bacteria Sinorhizobium meliloti and S. medicae. PLoS Genet. 8: e1002868.
    • (2012) PLoS Genet. , vol.8
    • Epstein, B.1
  • 31
    • 0035859832 scopus 로고    scopus 로고
    • 2-fixing endosymbiont Sinorhizobium meliloti
    • 2-fixing endosymbiont Sinorhizobium meliloti. Proc Natl Acad Sci U S A. 98:9889-9894.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 9889-9894
    • Finan, T.M.1
  • 32
    • 77949550491 scopus 로고    scopus 로고
    • Comparative genomics of VirR regulons in Clostridium perfringens strains
    • Frandi A, Mengoni A, Brilli M. 2010. Comparative genomics of VirR regulons in Clostridium perfringens strains. BMC Microbiol. 10:65.
    • (2010) BMC Microbiol. , vol.10 , pp. 65
    • Frandi, A.1    Mengoni, A.2    Brilli, M.3
  • 33
    • 79959240236 scopus 로고    scopus 로고
    • CONTIGuator: A bacterial genomes finishing tool for structural insights on draft genomes
    • Galardini M, Biondi E, Bazzicalupo M, Mengoni A. 2011. CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol Med. 6:11.
    • (2011) Source Code Biol Med. , vol.6 , pp. 11
    • Galardini, M.1    Biondi, E.2    Bazzicalupo, M.3    Mengoni, A.4
  • 34
    • 79955837064 scopus 로고    scopus 로고
    • Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti
    • Galardini M, et al. 2011. Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti. BMC Genomics 12:253.
    • (2011) BMC Genomics , vol.12 , pp. 253
    • Galardini, M.1
  • 35
    • 0035958746 scopus 로고    scopus 로고
    • The composite genome of the legume symbiont Sinorhizobium meliloti
    • Galibert F, et al. 2001. The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293:668-672.
    • (2001) Science , vol.293 , pp. 668-672
    • Galibert, F.1
  • 36
    • 58549105954 scopus 로고    scopus 로고
    • Molecular determinants of a symbiotic chronic infection
    • Gibson KE, Kobayashi H, Walker GC. 2008. Molecular determinants of a symbiotic chronic infection. Annu Rev Genet. 42:413-441.
    • (2008) Annu Rev Genet. , vol.42 , pp. 413-441
    • Gibson, K.E.1    Kobayashi, H.2    Walker, G.C.3
  • 37
    • 27944466762 scopus 로고    scopus 로고
    • Large-scale genetic variation of the symbiosisrequired megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains
    • Giuntini E, et al. 2005. Large-scale genetic variation of the symbiosisrequired megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains. BMC Genomics 6: 158.
    • (2005) BMC Genomics , vol.6 , pp. 158
    • Giuntini, E.1
  • 38
    • 0027291609 scopus 로고
    • A Rhizobium meliloti homolog of the Escherichia coli peptide-antibiotic transport protein SbmA is essential for bacteroid development
    • Glazebrook J, Ichige A, Walker GC. 1993. A Rhizobium meliloti homolog of the Escherichia coli peptide-antibiotic transport protein SbmA is essential for bacteroid development. Genes Dev. 7:1485-1497.
    • (1993) Genes Dev. , vol.7 , pp. 1485-1497
    • Glazebrook, J.1    Ichige, A.2    Walker, G.C.3
  • 39
    • 23944499633 scopus 로고    scopus 로고
    • Horizontal gene transfer, genome innovation and evolution
    • Gogarten JP, Townsend JP. 2005. Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol. 3:679-687.
    • (2005) Nat Rev Microbiol. , vol.3 , pp. 679-687
    • Gogarten, J.P.1    Townsend, J.P.2
  • 40
    • 70349799212 scopus 로고    scopus 로고
    • Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti
    • Guo H, Sun S, Eardly B, Finan T, Xu JP. 2009. Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti. Genome 52:862-875.
    • (2009) Genome , vol.52 , pp. 862-875
    • Guo, H.1    Sun, S.2    Eardly, B.3    Finan, T.4    Xu, J.P.5
  • 41
    • 0001905141 scopus 로고    scopus 로고
    • PAST: Paleontological Statistics Software Package for education and data analysis
    • Hammer 1, Harper DAT, Ryan PD. 2001. PAST: Paleontological Statistics Software Package for education and data analysis. Palaeontol Electron. 41:9.
    • (2001) Palaeontol Electron. , vol.41 , pp. 9
    • Hammer, J.1    Harper, D.A.T.2    Ryan, P.D.3
  • 43
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 44
    • 77952299957 scopus 로고    scopus 로고
    • Prodigal: Prokaryotic gene recognition and translation initiation site identification
    • Hyatt D, et al. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119.
    • (2010) BMC Bioinformatics , vol.11 , pp. 119
    • Hyatt, D.1
  • 45
    • 47549107328 scopus 로고    scopus 로고
    • Mutational analysis of the Sinorhizobium meliloti short-chain dehydrogenase/reductase family reveals substantial contribution to symbiosis and catabolic diversity
    • Jacob AI, et al. 2008. Mutational analysis of the Sinorhizobium meliloti short-chain dehydrogenase/reductase family reveals substantial contribution to symbiosis and catabolic diversity. Mol Plant Microbe Interact. 21:979-987.
    • (2008) Mol Plant Microbe Interact. , vol.21 , pp. 979-987
    • Jacob, A.I.1
  • 46
    • 0035106359 scopus 로고    scopus 로고
    • Genetic diversity of Sinorhizobium populations recovered from different Medicago varieties cultivated in Tunisian soils
    • Jebara M, Mhamdi R, Aouani ME, Ghrir R, Mars M. 2001. Genetic diversity of Sinorhizobium populations recovered from different Medicago varieties cultivated in Tunisian soils. Can J Microbiol. 47:139-147.
    • (2001) Can J Microbiol. , vol.47 , pp. 139-147
    • Jebara, M.1    Mhamdi, R.2    Aouani, M.E.3    Ghrir, R.4    Mars, M.5
  • 47
    • 14544277498 scopus 로고    scopus 로고
    • Ectoine-induced proteins in Sinorhizobium meliloti include an ectoine ABC-type transporter involved in osmoprotection and ectoine catabolism
    • Jebbar M, Sohn-Bösser L, Bremer E, Bernard TO, Blanco C. 2005. Ectoine-induced proteins in Sinorhizobium meliloti include an ectoine ABC-type transporter involved in osmoprotection and ectoine catabolism. J Bacteriol. 187:1293-1304.
    • (2005) J Bacteriol. , vol.187 , pp. 1293-1304
    • Jebbar, M.1    Sohn-Bösser, L.2    Bremer, E.3    Bernard, T.O.4    Blanco, C.5
  • 48
    • 78651281319 scopus 로고    scopus 로고
    • Genomic fluidity: An integrative view of gene diversity within microbial populations
    • Kislyuk A, Haegeman B, Bergman N, Weitz J. 2011. Genomic fluidity: an integrative view of gene diversity within microbial populations. BMC Genomics 12:32.
    • (2011) BMC Genomics , vol.12 , pp. 32
    • Kislyuk, A.1    Haegeman, B.2    Bergman, N.3    Weitz, J.4
  • 49
    • 62549132572 scopus 로고    scopus 로고
    • Darwinian evolution in the light of genomics
    • Koonin EV. 2009. Darwinian evolution in the light of genomics. Nucleic Acids Res. 37:1011-1034.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1011-1034
    • Koonin, E.V.1
  • 50
    • 80052313163 scopus 로고    scopus 로고
    • Are there laws of genome evolution?
    • Koonin EV. 2011. Are there laws of genome evolution? PLoS Comput Biol. 7:e1002173.
    • (2011) PLoS Comput Biol. , vol.7
    • Koonin, E.V.1
  • 51
    • 77953809541 scopus 로고    scopus 로고
    • Constraints and plasticity in genome and molecular-phenome evolution
    • Koonin EV, Wolf YI. 2010. Constraints and plasticity in genome and molecular-phenome evolution. Nat Rev Genet. 11:487-498.
    • (2010) Nat Rev Genet. , vol.11 , pp. 487-498
    • Koonin, E.V.1    Wolf, Y.I.2
  • 52
    • 0025245767 scopus 로고
    • Organization of the bacterial chromosome
    • Krawiec S, Riley M. 1990. Organization of the bacterial chromosome. Microbiol Rev. 54:502-539.
    • (1990) Microbiol Rev. , vol.54 , pp. 502-539
    • Krawiec, S.1    Riley, M.2
  • 53
    • 68149175229 scopus 로고    scopus 로고
    • The consequences of genetic drift for bacterial genome complexity
    • Kuo C-H, Moran NA, Ochman H. 2009. The consequences of genetic drift for bacterial genome complexity. Genome Res. 19: 1450-1454.
    • (2009) Genome Res. , vol.19 , pp. 1450-1454
    • Kuo, C.-H.1    Moran, N.A.2    Ochman, H.3
  • 54
    • 34250665888 scopus 로고    scopus 로고
    • RNAmmer: Consistent and rapid annotation of ribosomal RNA genes
    • Lagesen K, et al. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100-3108.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 3100-3108
    • Lagesen, K.1
  • 55
    • 34548846699 scopus 로고    scopus 로고
    • Evolution of the core and pan-genome of Streptococcus: Positive selection, recombination, and genome composition
    • Lefebure T, StanhopeMJ. 2007. Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol. 8:R71.
    • (2007) Genome Biol. , vol.8
    • Lefebure, T.1    Stanhope, M.J.2
  • 56
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Lowe TM, Eddy SR. 1999. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
    • (1999) Nucleic Acids Res. , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 57
    • 78149470831 scopus 로고    scopus 로고
    • Comparison of 61 sequenced Escherichia coli genomes
    • Lukjancenko O, Wassenaar TM, Ussery DW. 2010. Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol. 60:708-720.
    • (2010) Microb Ecol. , vol.60 , pp. 708-720
    • Lukjancenko, O.1    Wassenaar, T.M.2    Ussery, D.W.3
  • 58
    • 17444412589 scopus 로고    scopus 로고
    • Detecting amino acid sites under positive selection and purifying selection
    • Massingham T, Goldman N. 2005. Detecting amino acid sites under positive selection and purifying selection. Genetics 169:1753-1762.
    • (2005) Genetics , vol.169 , pp. 1753-1762
    • Massingham, T.1    Goldman, N.2
  • 60
    • 0020058862 scopus 로고
    • Physical and genetic characterization of symbiotic and auxotrophic mutants of Rhizobium meliloti induced by transposon Tn5 mutagenesis
    • Meade HM, Long SR, Ruvkun GB, Brown SE, Ausubel FM. 1982. Physical and genetic characterization of symbiotic and auxotrophic mutants of Rhizobium meliloti induced by transposon Tn5 mutagenesis. J Bacteriol. 149:114-122.
    • (1982) J Bacteriol. , vol.149 , pp. 114-122
    • Meade, H.M.1    Long, S.R.2    Ruvkun, G.B.3    Brown, S.E.4    Ausubel, F.M.5
  • 61
    • 43849099955 scopus 로고    scopus 로고
    • Microbiology in the post-genomic era
    • Medini D, et al. 2008. Microbiology in the post-genomic era. Nat Rev Microbiol. 6:419-430.
    • (2008) Nat Rev Microbiol. , vol.6 , pp. 419-430
    • Medini, D.1
  • 62
    • 77949512406 scopus 로고    scopus 로고
    • Tablet-next generation sequence assembly visualization
    • Milne I, et al. 2010. Tablet-next generation sequence assembly visualization. Bioinformatics 26:401-402.
    • (2010) Bioinformatics , vol.26 , pp. 401-402
    • Milne, I.1
  • 63
    • 35948957452 scopus 로고    scopus 로고
    • Metabolic capacity of Bacillus cereus strains ATCC 14579 and ATCC 10987 interlinked with comparative genomics
    • Mols M, de Been M, Zwietering MH, Moezelaar R, Abee T. 2007. Metabolic capacity of Bacillus cereus strains ATCC 14579 and ATCC 10987 interlinked with comparative genomics. Environ Microbiol. 9: 2933-2944.
    • (2007) Environ Microbiol. , vol.9 , pp. 2933-2944
    • Mols, M.1    De Been, M.2    Zwietering, M.H.3    Moezelaar, R.4    Abee, T.5
  • 65
  • 66
    • 80053366291 scopus 로고    scopus 로고
    • Interactive metagenomic visualization in a Web browser
    • Ondov B, Bergman N, Phillippy A. 2011. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12:385.
    • (2011) BMC Bioinformatics , vol.12 , pp. 385
    • Ondov, B.1    Bergman, N.2    Phillippy, A.3
  • 67
    • 0031959004 scopus 로고    scopus 로고
    • Influence of plant genotype on the selection of nodulating Sinorhizobium meliloti strains by Medicago sativa
    • Paffetti D, et al. 1998. Influence of plant genotype on the selection of nodulating Sinorhizobium meliloti strains by Medicago sativa. Antonie Van Leeuwenhoek 73:3-8.
    • (1998) Antonie Van Leeuwenhoek , vol.73 , pp. 3-8
    • Paffetti, D.1
  • 68
    • 0029999644 scopus 로고    scopus 로고
    • Genetic diversity of an Italian Rhizobium meliloti population from different Medicago sativa varieties
    • Paffetti D, Scotti C, Gnocchi S, Fancelli S, Bazzicalupo M. 1996. Genetic diversity of an Italian Rhizobium meliloti population from different Medicago sativa varieties. Appl Environ Microbiol. 62: 2279-2285.
    • (1996) Appl Environ Microbiol. , vol.62 , pp. 2279-2285
    • Paffetti, D.1    Scotti, C.2    Gnocchi, S.3    Fancelli, S.4    Bazzicalupo, M.5
  • 69
    • 0030203863 scopus 로고    scopus 로고
    • TreeView: An application to display phylogenetic trees on personal computers
    • Page RD. 1996. TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci. 12:357-358.
    • (1996) Comput Appl Biosci. , vol.12 , pp. 357-358
    • Page, R.D.1
  • 70
    • 80555140075 scopus 로고    scopus 로고
    • Scikit-learn: Machine learning in Python
    • Pedregosa F, et al. 2011. Scikit-learn: machine learning in Python. J Machine Learning Res. 12:2825-2830.
    • (2011) J Machine Learning Res. , vol.12 , pp. 2825-2830
    • Pedregosa, F.1
  • 72
    • 84861145419 scopus 로고    scopus 로고
    • Exploring the plant-associated bacterial communities in Medicago sativa L
    • Pini F, et al. 2012. Exploring the plant-associated bacterial communities in Medicago sativa L. BMC Microbiol. 12:78.
    • (2012) BMC Microbiol. , vol.12 , pp. 78
    • Pini, F.1
  • 73
    • 84055184708 scopus 로고    scopus 로고
    • Plant-bacteria association and symbiosis: Are there common genomic traits in Alphaproteobacteria?
    • Pini F, Galardini M, Bazzicalupo M, Mengoni A. 2011. Plant-bacteria association and symbiosis: are there common genomic traits in Alphaproteobacteria? Genes 2:1017-1032.
    • (2011) Genes , vol.2 , pp. 1017-1032
    • Pini, F.1    Galardini, M.2    Bazzicalupo, M.3    Mengoni, A.4
  • 74
    • 79953315166 scopus 로고    scopus 로고
    • Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes
    • Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T. 2011. Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res. 21:599-609.
    • (2011) Genome Res. , vol.21 , pp. 599-609
    • Popa, O.1    Hazkani-Covo, E.2    Landan, G.3    Martin, W.4    Dagan, T.5
  • 75
    • 33644857839 scopus 로고    scopus 로고
    • GenomeDiagram: A python package for the visualization of large-scale genomic data
    • Pritchard L,White JA, Birch PR, Toth IK. 2006. GenomeDiagram: a python package for the visualization of large-scale genomic data. Bioinformatics 22:616-617.
    • (2006) Bioinformatics , vol.22 , pp. 616-617
    • Pritchard, L.1    White, J.A.2    Birch, P.R.3    Toth, I.K.4
  • 76
    • 53849104729 scopus 로고    scopus 로고
    • The pangenome structure of Escherichia coli: Comparative genomic analysis of E. coli commensal and pathogenic isolates
    • Rasko DA, et al. 2008. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol. 190:6881-6893.
    • (2008) J Bacteriol. , vol.190 , pp. 6881-6893
    • Rasko, D.A.1
  • 77
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • Remm M, Storm CEV, Sonnhammer ELL. 2001. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol. 314:1041-1052.
    • (2001) J Mol Biol. , vol.314 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.V.2    Sonnhammer, E.L.L.3
  • 78
    • 0030479072 scopus 로고    scopus 로고
    • The common nodABC genes of Rhizobium meliloti are host-range determinants
    • Roche P, et al. 1996. The common nodABC genes of Rhizobium meliloti are host-range determinants. Proc Natl Acad Sci U S A. 93: 15305-15310.
    • (1996) Proc Natl Acad Sci U S A , vol.93 , pp. 15305-15310
    • Roche, P.1
  • 79
    • 0027985508 scopus 로고
    • Molecular and genetic characterization of the rhizopine catabolism (mocABRC) genes of Rhizobium meliloti L5-30
    • Rossbach S, Kulpa DA, Rossbach U, Bruijn FJ. 1994. Molecular and genetic characterization of the rhizopine catabolism (mocABRC) genes of Rhizobium meliloti L5-30. Mol Gen Genet. 245:11-24.
    • (1994) Mol Gen Genet. , vol.245 , pp. 11-24
    • Rossbach, S.1    Kulpa, D.A.2    Rossbach, U.3    Bruijn, F.J.4
  • 80
    • 79961211358 scopus 로고    scopus 로고
    • The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome
    • Schneiker-Bekel S, et al. 2011. The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome. J Biotechnol. 155:20-33.
    • (2011) J Biotechnol. , vol.155 , pp. 20-33
    • Schneiker-Bekel, S.1
  • 81
    • 66449136667 scopus 로고    scopus 로고
    • ABySS: A parallel assembler for short read sequence data
    • Simpson JT, et al. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res. 19:1117-1123.
    • (2009) Genome Res. , vol.19 , pp. 1117-1123
    • Simpson, J.T.1
  • 82
    • 72049088798 scopus 로고    scopus 로고
    • Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes
    • Soyer Y, Orsi R, Rodriguez-Rivera L, Sun Q,Wiedmann M. 2009. Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes. BMC Evol Biol. 9:264.
    • (2009) BMC Evol Biol. , vol.9 , pp. 264
    • Soyer, Y.1    Orsi, R.2    Rodriguez-Rivera, L.3    Sun Qwiedmann, M.4
  • 84
    • 77954202497 scopus 로고    scopus 로고
    • DendroPy: A Python library for phylogenetic computing
    • Sukumaran J, Holder MT. 2010. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26:1569-1571.
    • (2010) Bioinformatics , vol.26 , pp. 1569-1571
    • Sukumaran, J.1    Holder, M.T.2
  • 85
    • 52649157104 scopus 로고    scopus 로고
    • Diversity of Sinorhizobium strains nodulating Medicago sativa from different Iranian regions
    • Talebi Bedaf M, Bahar M, Saeidi G, Mengoni A, Bazzicalupo M. 2008. Diversity of Sinorhizobium strains nodulating Medicago sativa from different Iranian regions. FEMS Microbiol Lett. 288:40-46.
    • (2008) FEMS Microbiol Lett. , vol.288 , pp. 40-46
    • Talebi Bedaf, M.1    Bahar, M.2    Saeidi, G.3    Mengoni, A.4    Bazzicalupo, M.5
  • 86
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739.
    • (2011) Mol Biol Evol. , vol.28 , pp. 2731-2739
    • Tamura, K.1
  • 87
    • 0035162592 scopus 로고    scopus 로고
    • The COG database: New developments in phylogenetic classification of proteins from complete genomes
    • Tatusov RL, et al. 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29:22-28.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 22-28
    • Tatusov, R.L.1
  • 89
    • 84861893794 scopus 로고    scopus 로고
    • Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations
    • Tian CF, et al. 2012. Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations. Proc Natl Acad Sci U S A. 109:8629-8634.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 8629-8634
    • Tian, C.F.1
  • 90
    • 79952005629 scopus 로고    scopus 로고
    • Genetic diversity and salt tolerance of Sinorhizobium populations from two Tunisian soils
    • Trabelsi D, Mengoni A, Aouani ME, Bazzicalupo M, Mhamdi R. 2010. Genetic diversity and salt tolerance of Sinorhizobium populations from two Tunisian soils. Ann Microbiol. 60(3):541-547.
    • (2010) Ann Microbiol. , vol.60 , Issue.3 , pp. 541-547
    • Trabelsi, D.1    Mengoni, A.2    Aouani, M.E.3    Bazzicalupo, M.4    Mhamdi, R.5
  • 91
    • 60349117029 scopus 로고    scopus 로고
    • Development of real-time PCR assay for detection and quantification of Sinorhizobium meliloti in soil and plant tissue
    • Trabelsi D, Pini F, Aouani ME, Bazzicalupo M, Mengoni A. 2009. Development of real-time PCR assay for detection and quantification of Sinorhizobium meliloti in soil and plant tissue. Lett Appl Microbiol. 48:355-361.
    • (2009) Lett Appl Microbiol. , vol.48 , pp. 355-361
    • Trabelsi, D.1    Pini, F.2    Aouani, M.E.3    Bazzicalupo, M.4    Mengoni, A.5
  • 92
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556.
    • (1997) Comput Appl Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1
  • 94
    • 0034800374 scopus 로고    scopus 로고
    • InterProScan-an integration platformfor the signature-recognition methods in InterPro
    • Zdobnov EM, Apweiler R. 2001. InterProScan-an integration platformfor the signature-recognition methods in InterPro. Bioinformatics 17: 847-848.
    • (2001) Bioinformatics , vol.17 , pp. 847-848
    • Zdobnov, E.M.1    Apweiler, R.2
  • 95
    • 33751342650 scopus 로고    scopus 로고
    • Statistical tests for detecting positive selection by utilizing high-frequency variants
    • Zeng K, Fu Y-X, Shi S, Wu C-I. 2006. Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics 174: 1431-1439.
    • (2006) Genetics , vol.174 , pp. 1431-1439
    • Zeng, K.1    Fu, Y.-X.2    Shi, S.3    Wu, C.-I.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.