메뉴 건너뛰기




Volumn 5, Issue 3, 2013, Pages 599-605

Sequence context of indel mutations and their effect on protein evolution in a bacterial endosymbiont

Author keywords

Comparative genomics; Compensatory indels; Genome reduction; Molecular evolution; Purifying selection; Sequence repeats

Indexed keywords

BACTERIA (MICROORGANISMS); CAMPONOTUS; CANDIDATUS BLOCHMANNIA CHROMAIODES;

EID: 84876580349     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evt033     Document Type: Article
Times cited : (36)

References (33)
  • 1
    • 77954272855 scopus 로고    scopus 로고
    • TranslatorX: Multiple alignment of nucleotide sequences guided by amino acid translations
    • Abascal F, Zardoya R, Telford MJ. 2010. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res. 38:W7-W13.
    • (2010) Nucleic Acids Res. , vol.38
    • Abascal, F.1    Zardoya, R.2    Telford, M.J.3
  • 4
    • 1642308878 scopus 로고    scopus 로고
    • Host-symbiont stability and fast evolutionary rates in an ant-bacterium association: Cospeciation of Camponotus species and their endosymbionts, Candidatus blochmannia
    • Degnan PH, Lazarus AB, Brock CD, Wernegreen JJ. 2004. Host-symbiont stability and fast evolutionary rates in an ant-bacterium association: cospeciation of Camponotus species and their endosymbionts, Candidatus blochmannia. Syst Biol. 53:95-110.
    • (2004) Syst Biol. , vol.53 , pp. 95-110
    • Degnan, P.H.1    Lazarus, A.B.2    Brock, C.D.3    Wernegreen, J.J.4
  • 5
    • 23744515783 scopus 로고    scopus 로고
    • Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects
    • Degnan PH, Lazarus AB, Wernegreen JJ. 2005. Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects. Genome Res. 15:1023-1033.
    • (2005) Genome Res. , vol.15 , pp. 1023-1033
    • Degnan, P.H.1    Lazarus, A.B.2    Wernegreen, J.J.3
  • 6
    • 80053458871 scopus 로고    scopus 로고
    • Sequence conservation and functional constraint on intergenic spacers in reduced genomes of the obligate symbiont Buchnera
    • Degnan PH, Ochman H, Moran NA. 2011. Sequence conservation and functional constraint on intergenic spacers in reduced genomes of the obligate symbiont Buchnera. PLoS Genet. 7:e1002252.
    • (2011) PLoS Genet. , vol.7
    • Degnan, P.H.1    Ochman, H.2    Moran, N.A.3
  • 7
    • 77957233773 scopus 로고    scopus 로고
    • The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection
    • Fletcher W, Yang Z. 2010. The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol. 27:2257-2267.
    • (2010) Mol Biol Evol. , vol.27 , pp. 2257-2267
    • Fletcher, W.1    Yang, Z.2
  • 8
    • 58149191274 scopus 로고    scopus 로고
    • Rfam: Updates to the RNA families database
    • Gardner PP, et al. 2009. Rfam: updates to the RNA families database. Nucleic Acids Res. 37:D136-D140.
    • (2009) Nucleic Acids Res. , vol.37
    • Gardner, P.P.1
  • 9
    • 33846252244 scopus 로고    scopus 로고
    • Genome reduction of the aphid endosymbiont Buchnera aphidicola in a recent evolutionary time scale
    • Gomez-Valero L, Silva FJ, Christophe Simon J, Latorre A. 2007. Genome reduction of the aphid endosymbiont Buchnera aphidicola in a recent evolutionary time scale. Gene 389:87-95.
    • (2007) Gene , vol.389 , pp. 87-95
    • Gomez-Valero, L.1    Silva, F.J.2    Christophe Simon, J.3    Latorre, A.4
  • 10
    • 52649174233 scopus 로고    scopus 로고
    • Patterns and rates of nucleotide substitution, insertion and deletion in the endosymbiont of ants Blochmannia floridanus
    • Gomez-Valero L, et al. 2008. Patterns and rates of nucleotide substitution, insertion and deletion in the endosymbiont of ants Blochmannia floridanus. Mol Ecol. 17:4382-4392.
    • (2008) Mol Ecol. , vol.17 , pp. 4382-4392
    • Gomez-Valero, L.1
  • 11
    • 84862777146 scopus 로고    scopus 로고
    • Predicting the effects of frameshifting indels
    • Hu J, Ng PC. 2012. Predicting the effects of frameshifting indels. Genome Biol. 13:R9.
    • (2012) Genome Biol. , vol.13
    • Hu, J.1    Ng, P.C.2
  • 12
    • 84858402388 scopus 로고    scopus 로고
    • The effects of alignment error and alignment filtering on the sitewise detection of positive selection
    • Jordan G, Goldman N. 2012. The effects of alignment error and alignment filtering on the sitewise detection of positive selection. Mol Biol Evol. 29:1125-1139.
    • (2012) Mol Biol Evol. , vol.29 , pp. 1125-1139
    • Jordan, G.1    Goldman, N.2
  • 13
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33: 511-518.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 14
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254.
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 15
    • 2942538300 scopus 로고    scopus 로고
    • Versatile and open software for comparing large genomes
    • Kurtz S, et al. 2004. Versatile and open software for comparing large genomes. Genome Biol. 5:R12.
    • (2004) Genome Biol. , vol.5
    • Kurtz, S.1
  • 16
    • 84863090410 scopus 로고    scopus 로고
    • Insertions and deletions trigger adaptive walks in Drosophila proteins
    • Leushkin EV, Bazykin GA, Kondrashov AS. 2012. Insertions and deletions trigger adaptive walks in Drosophila proteins. Proc Biol Sci. 279: 3075-3082.
    • (2012) Proc Biol Sci. , vol.279 , pp. 3075-3082
    • Leushkin, E.V.1    Bazykin, G.A.2    Kondrashov, A.S.3
  • 17
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 18
    • 77955394202 scopus 로고    scopus 로고
    • VariantClassifier: A hierarchical variant classifier for annotated genomes
    • Li K, Stockwell TB. 2010. VariantClassifier: a hierarchical variant classifier for annotated genomes. BMC Res Notes. 3:191.
    • (2010) BMC Res Notes. , vol.3 , pp. 191
    • Li, K.1    Stockwell, T.B.2
  • 19
    • 77956295988 scopus 로고    scopus 로고
    • The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna A, et al. 2010. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-1303.
    • (2010) Genome Res. , vol.20 , pp. 1297-1303
    • McKenna, A.1
  • 20
    • 58449125407 scopus 로고    scopus 로고
    • Genomics and evolution of heritable bacterial symbionts
    • Moran NA, McCutcheon JP, Nakabachi A. 2008. Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet. 42:165-190.
    • (2008) Annu Rev Genet. , vol.42 , pp. 165-190
    • Moran, N.A.1    McCutcheon, J.P.2    Nakabachi, A.3
  • 21
    • 58449126084 scopus 로고    scopus 로고
    • The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria
    • Moran NA, McLaughlin HJ, Sorek R. 2009. The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323:379-382.
    • (2009) Science , vol.323 , pp. 379-382
    • Moran, N.A.1    McLaughlin, H.J.2    Sorek, R.3
  • 22
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841-842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 23
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European molecular biology open software suite
    • Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16:276-277.
    • (2000) Trends Genet. , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 24
    • 54449100127 scopus 로고    scopus 로고
    • Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts
    • Tamas I, et al. 2008. Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts. Proc Natl Acad Sci U S A. 105: 14934-14939.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 14934-14939
    • Tamas, I.1
  • 25
    • 51349155028 scopus 로고    scopus 로고
    • Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes
    • Tian D, et al. 2008. Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. Nature 455:105-108.
    • (2008) Nature , vol.455 , pp. 105-108
    • Tian, D.1
  • 27
    • 83355170629 scopus 로고    scopus 로고
    • Reduced selective constraint in endosymbionts: Elevation in radical amino acid replacements occurs genome-wide
    • Wernegreen JJ. 2011. Reduced selective constraint in endosymbionts: elevation in radical amino acid replacements occurs genome-wide. PLoS One 6:e28905.
    • (2011) PLoS One , vol.6
    • Wernegreen, J.J.1
  • 28
    • 76049092025 scopus 로고    scopus 로고
    • One nutritional symbiosis begat another: Phylogenetic evidence that the ant tribe Camponotini acquired Blochmannia by tending sap-feeding insects
    • Wernegreen JJ, Kauppinen SN, Brady SG, Ward PS. 2009. One nutritional symbiosis begat another: phylogenetic evidence that the ant tribe Camponotini acquired Blochmannia by tending sap-feeding insects. BMC Evol Biol. 9:292.
    • (2009) BMC Evol Biol. , vol.9 , pp. 292
    • Wernegreen, J.J.1    Kauppinen, S.N.2    Brady, S.G.3    Ward, P.S.4
  • 29
    • 0036667441 scopus 로고    scopus 로고
    • Small genome of Candidatus Blochmannia, the bacterial endosymbiont of Camponotus, implies irreversible specialization to an intracellular lifestyle
    • Wernegreen JJ, Lazarus AB, Degnan PH. 2002. Small genome of Candidatus Blochmannia, the bacterial endosymbiont of Camponotus, implies irreversible specialization to an intracellular lifestyle. Microbiology 148:2551-2556.
    • (2002) Microbiology , vol.148 , pp. 2551-2556
    • Wernegreen, J.J.1    Lazarus, A.B.2    Degnan, P.H.3
  • 30
    • 84860009975 scopus 로고    scopus 로고
    • Accurate reconstruction of insertion-deletion histories by statistical phylogenetics
    • Westesson O, Lunter G, Paten B, Holmes I. 2012. Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. PLoS One 7: e34572.
    • (2012) PLoS One , vol.7
    • Westesson, O.1    Lunter, G.2    Paten, B.3    Holmes, I.4
  • 31
    • 78649588858 scopus 로고    scopus 로고
    • Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist
    • Williams LE, Wernegreen JJ. 2010. Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist. BMC Genomics 11:687.
    • (2010) BMC Genomics , vol.11 , pp. 687
    • Williams, L.E.1    Wernegreen, J.J.2
  • 32
    • 84862989867 scopus 로고    scopus 로고
    • Purifying selection, sequence composition, and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont
    • Williams LE, Wernegreen JJ. 2012. Purifying selection, sequence composition, and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont. Genome Biol Evol. 4:44-51.
    • (2012) Genome Biol Evol. , vol.4 , pp. 44-51
    • Williams, L.E.1    Wernegreen, J.J.2
  • 33
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.