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Volumn 11, Issue 1, 2011, Pages

Loss of genes for DNA recombination and repair in the reductive genome evolution of thioautotrophic symbionts of Calyptogena clams

Author keywords

[No Author keywords available]

Indexed keywords

BIVALVE; CLADISTICS; EVOLUTIONARY BIOLOGY; GENETIC ANALYSIS; GENOME; POLYMERASE CHAIN REACTION; RECOMBINATION; SYMBIONT;

EID: 80053438060     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-285     Document Type: Article
Times cited : (17)

References (45)
  • 1
    • 0035749612 scopus 로고    scopus 로고
    • The process of genome shrinkage in the obligate symbiont Buchnera aphidicola
    • research/\0054.1-12
    • The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. Moran NA, Mira A, Genome Biology 2001 2 12 research/\0054.1-12
    • (2001) Genome Biology , vol.2 , Issue.12
    • Moran, N.A.1    Mira, A.2
  • 2
    • 0035479142 scopus 로고    scopus 로고
    • Deletional bias and the evolution of bacterial genomes
    • DOI 10.1016/S0168-9525(01)02447-7, PII S0168952501024477
    • Deletional bias and the evolution of bacterial genomes. Mira A, Ochman H, Moran NA, Trends Genet 2001 17 10 589 596 10.1016/S0168-9525(01)02447-7 11585665 (Pubitemid 32918301)
    • (2001) Trends in Genetics , vol.17 , Issue.10 , pp. 589-596
    • Mira, A.1    Ochman, H.2    Moran, N.A.3
  • 3
    • 0242386452 scopus 로고    scopus 로고
    • Tracing the evolution of gene loss in obligate bacterial symbionts
    • DOI 10.1016/j.mib.2003.08.001
    • Tracing the evolution of gene loss in obligate bacterial symbionts. Moran NA, Current Opinion in Microbiology 2003 6 5 512 518 10.1016/j.mib.2003.08.001 14572545 (Pubitemid 37345418)
    • (2003) Current Opinion in Microbiology , vol.6 , Issue.5 , pp. 512-518
    • Moran, N.A.1
  • 4
    • 68249126127 scopus 로고    scopus 로고
    • Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont
    • 19609354
    • Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont. McCutcheon JP, McDonald BR, Moran NA, Plos Genetics 2009 5 7 1000565. 19609354
    • (2009) Plos Genetics , vol.5 , Issue.7 , pp. 51000565
    • McCutcheon, J.P.1    McDonald, B.R.2    Moran, N.A.3
  • 5
    • 55449115425 scopus 로고    scopus 로고
    • Comparative and evolutionary analysis of the bacterial homologous recombination systems
    • Comparative and evolutionary analysis of the bacterial homologous recombination systems. Rocha EPC, Cornet E, Michel B, Plos Genetics 2005 1 2 247 259
    • (2005) Plos Genetics , vol.1 , Issue.2 , pp. 247-259
    • Rocha, E.P.C.1    Cornet, E.2    Michel, B.3
  • 6
    • 66249088027 scopus 로고    scopus 로고
    • For absent friends: Life without recombination in mutualistic gamma-proteobacteria
    • 10.1016/j.tim.2009.03.005 19464894
    • For absent friends: life without recombination in mutualistic gamma-proteobacteria. Sharples GJ, Trends Microbiol 2009 17 6 233 242 10.1016/j.tim.2009.03.005 19464894
    • (2009) Trends Microbiol , vol.17 , Issue.6 , pp. 233-242
    • Sharples, G.J.1
  • 8
    • 43049167550 scopus 로고    scopus 로고
    • Reductive genome evolution in chemoautotrophic intracellular symbionts of deep-sea Calyptogena clams
    • 10.1007/s00792-008-0141-2 18305898
    • Reductive genome evolution in chemoautotrophic intracellular symbionts of deep-sea Calyptogena clams. Kuwahara H, Takaki Y, Yoshida T, Shimamura S, Takishita K, Reimer JD, Kato C, Maruyama T, Extremophiles 2008 12 3 365 374 10.1007/s00792-008-0141-2 18305898
    • (2008) Extremophiles , vol.12 , Issue.3 , pp. 365-374
    • Kuwahara, H.1    Takaki, Y.2    Yoshida, T.3    Shimamura, S.4    Takishita, K.5    Reimer, J.D.6    Kato, C.7    Maruyama, T.8
  • 9
    • 58449126084 scopus 로고    scopus 로고
    • The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria
    • 10.1126/science.1167140 19150844
    • The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Moran NA, McLaughlin HJ, Sorek R, Science 2009 323 5912 379 382 10.1126/science.1167140 19150844
    • (2009) Science , vol.323 , Issue.5912 , pp. 379-382
    • Moran, N.A.1    McLaughlin, H.J.2    Sorek, R.3
  • 10
    • 23944506540 scopus 로고    scopus 로고
    • Chemosynthetic endosymbioses: Adaptations to oxic-anoxic interfaces
    • DOI 10.1016/j.tim.2005.07.007, PII S0966842X05001964
    • Chemosynthetic endosymbioses: adaptations to oxic-anoxic interfaces. Stewart FJ, Newton IL, Cavanaugh CM, Trends Microbiol 2005 13 9 439 448 10.1016/j.tim.2005.07.007 16054816 (Pubitemid 41207178)
    • (2005) Trends in Microbiology , vol.13 , Issue.9 , pp. 439-448
    • Stewart, F.J.1    Newton, I.L.G.2    Cavanaugh, C.M.3
  • 11
    • 0001276853 scopus 로고
    • Occurrence of Bacteria in the Primary Oocytes of Vesicomyid Clam Calyptogena-Soyoae
    • Occurrence of Bacteria in the Primary Oocytes of Vesicomyid Clam Calyptogena-Soyoae. Endow K, Ohta S, Marine Ecology-Progress Series 1990 64 3 309 311
    • (1990) Marine Ecology-Progress Series , vol.64 , Issue.3 , pp. 309-311
    • Endow, K.1    Ohta, S.2
  • 12
    • 0027211060 scopus 로고
    • Transovarial inheritance of endosymbiotic bacteria in clams inhabiting deep-sea hydrothermal vents and cold seeps
    • Transovarial Inheritance of Endosymbiotic Bacteria in Clams Inhabiting Deep-Sea Hydrothermal Vents and Cold Seeps. Cary SC, Giovannoni SJ, Proceedings of the National Academy of Sciences of the United States of America 1993 90 12 5695 5699 10.1073/pnas.90.12.5695 8100068 (Pubitemid 23176228)
    • (1993) Proceedings of the National Academy of Sciences of the United States of America , vol.90 , Issue.12 , pp. 5695-5699
    • Cary, S.C.1    Giovannoni, S.J.2
  • 14
    • 40849142148 scopus 로고    scopus 로고
    • Lateral symbiont acquisition in a maternally transmitted chemosynthetic clam endosymbiosis
    • DOI 10.1093/molbev/msn010
    • Lateral symbiont acquisition in a maternally transmitted chemosynthetic clam endosymbiosis. Stewart FJ, Young CR, Cavanaugh CM, Mol Biol Evol 2008 25 4 673 687 10.1093/molbev/msn010 18192696 (Pubitemid 351398323)
    • (2008) Molecular Biology and Evolution , vol.25 , Issue.4 , pp. 673-687
    • Stewart, F.J.1    Young, C.R.2    Cavanaugh, C.M.3
  • 15
    • 80054979342 scopus 로고    scopus 로고
    • Vesicomyid Fauna in the Chishima (Kurile) Trench: Occurrences of a New Taxon and Calyptogena extenta
    • Vesicomyid Fauna in the Chishima (Kurile) Trench: Occurrences of a New Taxon and Calyptogena extenta. Okutani T, Koshi-ishi T, Sato T, Imai T, Kato C, VENUS 2009 68 1-2 15 25
    • (2009) VENUS , vol.68 , Issue.1-2 , pp. 15-25
    • Okutani, T.1    Koshi-Ishi, T.2    Sato, T.3    Imai, T.4    Kato, C.5
  • 19
    • 2942630097 scopus 로고    scopus 로고
    • Encoded errors: Mutations and rearrangements mediated by misalignment at repetitive DNA sequences
    • DOI 10.1111/j.1365-2958.2004.04076.x
    • Encoded errors: mutations and rearrangements mediated by misalignment at repetitive DNA sequences. Lovett ST, Molecular Microbiology 2004 52 5 1243 1253 10.1111/j.1365-2958.2004.04076.x 15165229 (Pubitemid 38746300)
    • (2004) Molecular Microbiology , vol.52 , Issue.5 , pp. 1243-1253
    • Lovett, S.T.1
  • 21
    • 0042073066 scopus 로고    scopus 로고
    • Loss of DNA recombinational repair enzymes in the initial stages of genome degeneration
    • DOI 10.1093/molbev/msg138
    • Loss of DNA recombinational repair enzymes in the initial stages of genome degeneration. Dale C, Wang B, Moran N, Ochman H, Mol Biol Evol 2003 20 8 1188 1194 10.1093/molbev/msg138 12777518 (Pubitemid 36961237)
    • (2003) Molecular Biology and Evolution , vol.20 , Issue.8 , pp. 1188-1194
    • Dale, C.1    Wang, B.2    Moran, N.3    Ochman, H.4
  • 23
    • 0037803483 scopus 로고    scopus 로고
    • An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: From duplications to genome reduction
    • DOI 10.1101/gr.966203
    • An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: From duplications to genome reduction. Rocha EPC, Genome Research 2003 13 6 1123 1132 10.1101/gr.966203 12743022 (Pubitemid 36764192)
    • (2003) Genome Research , vol.13 , Issue.6 A , pp. 1123-1132
    • Rocha, E.P.C.1
  • 24
    • 4444308700 scopus 로고    scopus 로고
    • Crystal structures of Escherichia coli RecA in a compressed helical filament
    • DOI 10.1016/j.jmb.2004.07.091, PII S0022283604009465
    • Crystal structures of Escherichia coli RecA in a compressed helical filament. Xing X, Bell CE, J Mol Biol 2004 342 5 1471 1485 10.1016/j.jmb.2004. 07.091 15364575 (Pubitemid 39208673)
    • (2004) Journal of Molecular Biology , vol.342 , Issue.5 , pp. 1471-1485
    • Xing, X.1    Bell, C.E.2
  • 25
    • 0031763884 scopus 로고    scopus 로고
    • MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily
    • DOI 10.1038/4168
    • MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily. Guan Y, Manuel RC, Arvai AS, Parikh SS, Mol CD, Miller JH, Lloyd S, Tainer JA, Nat Struct Biol 1998 5 12 1058 1064 10.1038/4168 9846876 (Pubitemid 28546269)
    • (1998) Nature Structural Biology , vol.5 , Issue.12 , pp. 1058-1064
    • Guan, Y.1    Manuel, R.C.2    Arvai, A.S.3    Parikh, S.S.4    Mol, C.D.5    Miller, J.H.6    Lloyd, R.S.7    Tainer, J.A.8
  • 26
    • 1342304229 scopus 로고    scopus 로고
    • Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase
    • DOI 10.1038/nature02306
    • Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase. Fromme JC, Banerjee A, Huang SJ, Verdine GL, Nature 2004 427 6975 652 656 10.1038/nature02306 14961129 (Pubitemid 38248487)
    • (2004) Nature , vol.427 , Issue.6975 , pp. 652-656
    • Christopher Fromme, J.1    Banerjee, A.2    Huang, S.J.3    Verdine, G.L.4
  • 27
    • 56649099178 scopus 로고    scopus 로고
    • Whole-genome mutational biases in bacteria
    • 10.1073/pnas.0804445105 19001264
    • Whole-genome mutational biases in bacteria. Lind PA, Andersson DI, Proc Natl Acad Sci USA 2008 105 46 17878 17883 10.1073/pnas.0804445105 19001264
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.46 , pp. 17878-17883
    • Lind, P.A.1    Andersson, D.I.2
  • 28
    • 66249089033 scopus 로고    scopus 로고
    • Evidence for homologous recombination in intracellular chemosynthetic clam symbionts
    • 10.1093/molbev/msp049 19289597
    • Evidence for homologous recombination in intracellular chemosynthetic clam symbionts. Stewart FJ, Young CR, Cavanaugh CM, Mol Biol Evol 2009 26 6 1391 1404 10.1093/molbev/msp049 19289597
    • (2009) Mol Biol Evol , vol.26 , Issue.6 , pp. 1391-1404
    • Stewart, F.J.1    Young, C.R.2    Cavanaugh, C.M.3
  • 29
    • 78049445172 scopus 로고    scopus 로고
    • Evidence that mutation is universally biased towards at in bacteria
    • 10.1371/journal.pgen.1001115 20838599
    • Evidence that mutation is universally biased towards AT in bacteria. Hershberg R, Petrov DA, PLoS Genet 2010 6 9 1001115 10.1371/journal.pgen.1001115 20838599
    • (2010) PLoS Genet , vol.6 , Issue.9 , pp. 51001115
    • Hershberg, R.1    Petrov, D.A.2
  • 30
    • 78049425463 scopus 로고    scopus 로고
    • Evidence of selection upon genomic GC-content in bacteria
    • 10.1371/journal.pgen.1001107 20838593
    • Evidence of selection upon genomic GC-content in bacteria. Hildebrand F, Meyer A, Eyre-Walker A, PLoS Genet 2010 6 9 1001107 10.1371/journal.pgen.1001107 20838593
    • (2010) PLoS Genet , vol.6 , Issue.9 , pp. 51001107
    • Hildebrand, F.1    Meyer, A.2    Eyre-Walker, A.3
  • 31
    • 78049437494 scopus 로고    scopus 로고
    • Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria?
    • 10.1371/journal.pgen.1001104 20838590
    • Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria? Rocha EP, Feil EJ, PLoS Genet 2010 6 9 1001104 10.1371/journal.pgen.1001104 20838590
    • (2010) PLoS Genet , vol.6 , Issue.9 , pp. 51001104
    • Rocha, E.P.1    Feil, E.J.2
  • 34
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Katoh K, Misawa K, Kuma K, Miyata T, Nucleic Acids Res 2002 30 14 3059 3066 10.1093/nar/gkf436 12136088 (Pubitemid 34851225)
    • (2002) Nucleic Acids Research , vol.30 , Issue.14 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.-I.3    Miyata, T.4
  • 35
    • 44149125756 scopus 로고    scopus 로고
    • Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework
    • DOI 10.1186/1471-2105-9-212
    • Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. Katoh K, Toh H, BMC Bioinformatics 2008 9 212 10.1186/1471-2105-9-212 18439255 (Pubitemid 351715980)
    • (2008) BMC Bioinformatics , vol.9 , pp. 212
    • Katoh, K.1    Toh, H.2
  • 36
    • 80054983637 scopus 로고    scopus 로고
    • Sequence Alignment Editor v2.0
    • Sequence Alignment Editor v2.0 [ http://iubio.bio.indiana.edu/soft/ iubionew/molbio/dna/analysis/Pist/main.html
  • 38
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • DOI 10.1093/molbev/msm092
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Tamura K, Dudley J, Nei M, Kumar S, Mol Biol Evol 2007 24 8 1596 1599 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 40
    • 0031773680 scopus 로고    scopus 로고
    • MODELTEST: Testing the model of DNA substitution
    • MODELTEST: testing the model of DNA substitution. Posada D, Crandall KA, Bioinformatics 1998 14 9 817 818 10.1093/bioinformatics/14.9.817 9918953 (Pubitemid 28552116)
    • (1998) Bioinformatics , vol.14 , Issue.9 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 42
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • DOI 10.1093/bioinformatics/btg180
    • MrBayes 3: Bayesian phylogenetic inference under mixed models. Ronquist F, Huelsenbeck JP, Bioinformatics 2003 19 12 1572 1574 10.1093/bioinformatics/ btg180 12912839 (Pubitemid 37038874)
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 43
  • 44
    • 0035861456 scopus 로고    scopus 로고
    • Bayesian inference of phylogeny and its impact on evolutionary biology
    • DOI 10.1126/science.1065889
    • Bayesian inference of phylogeny and its impact on evolutionary biology. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP, Science 2001 294 5550 2310 2314 10.1126/science.1065889 11743192 (Pubitemid 33140548)
    • (2001) Science , vol.294 , Issue.5550 , pp. 2310-2314
    • Huelsenbeck, J.P.1    Ronquist, F.2    Nielsen, R.3    Bollback, J.P.4
  • 45
    • 0037398368 scopus 로고    scopus 로고
    • LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
    • DOI 10.1101/gr.926603
    • LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S, Genome Res 2003 13 4 721 731 10.1101/gr.926603 12654723 (Pubitemid 36511930)
    • (2003) Genome Research , vol.13 , Issue.4 , pp. 721-731
    • Brudno, M.1    Do, C.B.2    Cooper, G.M.3    Kim, M.F.4    Davydov, E.5    Green, E.D.6    Sidow, A.7    Batzoglou, S.8


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