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Volumn 38, Issue 2, 2015, Pages 79-83

Large-scale evaluation of experimentally determined DNA G+C contents with whole genome sequences of prokaryotes

Author keywords

Average nucleotide identity; DNA G+C content; Prokaryote taxonomy; Whole genome sequences

Indexed keywords

CYTOSINE; DNA; GUANINE; NUCLEOTIDE; ARCHAEAL DNA; BACTERIAL DNA;

EID: 84940162621     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2014.11.008     Document Type: Article
Times cited : (13)

References (33)
  • 2
    • 84908219488 scopus 로고
    • Statistical methods for assessing agreement between two methods of clinical measurement
    • Bland J.M., Altman D.G. Statistical methods for assessing agreement between two methods of clinical measurement. Lancet 1986, 1:307-310.
    • (1986) Lancet , vol.1 , pp. 307-310
    • Bland, J.M.1    Altman, D.G.2
  • 3
    • 84876936831 scopus 로고    scopus 로고
    • Effects of GC bias in next-generation-sequencing data on de novo genome assembly
    • Chen Y.C., Liu T.L., Yu C.H., Chiang T.Y., Hwang C.C. Effects of GC bias in next-generation-sequencing data on de novo genome assembly. PLOS ONE 2013, 8:e62856.
    • (2013) PLOS ONE , vol.8 , pp. e62856
    • Chen, Y.C.1    Liu, T.L.2    Yu, C.H.3    Chiang, T.Y.4    Hwang, C.C.5
  • 4
    • 33744772295 scopus 로고    scopus 로고
    • Estimation of prokaryote genomic DNA G+C content by sequencing universally conserved genes
    • Fournier P.E., Suhre K., Fournous G., Raoult D. Estimation of prokaryote genomic DNA G+C content by sequencing universally conserved genes. Int. J. Syst. Evol. Microbiol. 2006, 56:1025-1029.
    • (2006) Int. J. Syst. Evol. Microbiol. , vol.56 , pp. 1025-1029
    • Fournier, P.E.1    Suhre, K.2    Fournous, G.3    Raoult, D.4
  • 6
    • 0002771212 scopus 로고    scopus 로고
    • Towards a practical species concept for cultivable bacteria
    • Chapman and Hall, London, M.F. Clarridge, H.A. Dawah, M.R. Wilson (Eds.)
    • Goodfellow M., Manfio G.P., Chun J. Towards a practical species concept for cultivable bacteria. Species: The Units of Biodiversity 1997, 25-29. Chapman and Hall, London. M.F. Clarridge, H.A. Dawah, M.R. Wilson (Eds.).
    • (1997) Species: The Units of Biodiversity , pp. 25-29
    • Goodfellow, M.1    Manfio, G.P.2    Chun, J.3
  • 8
    • 67349135982 scopus 로고    scopus 로고
    • A plot of G plus C content against sequence length of 640 bacterial chromosomes shows the points are widely scattered in the upper triangular area
    • Guo F.B., Lin H., Huang J. A plot of G plus C content against sequence length of 640 bacterial chromosomes shows the points are widely scattered in the upper triangular area. Chromosome Res. 2009, 17:359-364.
    • (2009) Chromosome Res. , vol.17 , pp. 359-364
    • Guo, F.B.1    Lin, H.2    Huang, J.3
  • 9
    • 78049445172 scopus 로고    scopus 로고
    • Evidence that mutation is universally biased towards AT in bacteria
    • Hershberg R., Petrov D.A. Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet. 2010, 6:e1001115.
    • (2010) PLoS Genet. , vol.6 , pp. e1001115
    • Hershberg, R.1    Petrov, D.A.2
  • 10
    • 77956834538 scopus 로고
    • Determination of DNA base composition
    • Academic Press, London, G. Gottschalk (Ed.)
    • Johnson J.L. Determination of DNA base composition. Methods in Microbiology 1985, 1-31. Academic Press, London. G. Gottschalk (Ed.).
    • (1985) Methods in Microbiology , pp. 1-31
    • Johnson, J.L.1
  • 11
    • 84893511241 scopus 로고    scopus 로고
    • Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
    • Kim M., Oh H.-S., Park S.-C., Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int. J. Syst. Evol. Microbiol. 2014, 64:346-351.
    • (2014) Int. J. Syst. Evol. Microbiol. , vol.64 , pp. 346-351
    • Kim, M.1    Oh, H.-S.2    Park, S.-C.3    Chun, J.4
  • 12
    • 63949083912 scopus 로고    scopus 로고
    • Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
    • Kozarewa I., Ning Z., Quail M.A., Sanders M.J., Berriman M., Turner D.J. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat. Methods 2009, 6:291-295.
    • (2009) Nat. Methods , vol.6 , pp. 291-295
    • Kozarewa, I.1    Ning, Z.2    Quail, M.A.3    Sanders, M.J.4    Berriman, M.5    Turner, D.J.6
  • 13
    • 39549097083 scopus 로고    scopus 로고
    • Why Bland-Altman plots should use X, not (Y+X)/2 when X is a reference method
    • Krouwer J.S. Why Bland-Altman plots should use X, not (Y+X)/2 when X is a reference method. Stat. Med. 2008, 27:778-780.
    • (2008) Stat. Med. , vol.27 , pp. 778-780
    • Krouwer, J.S.1
  • 14
  • 15
    • 33748768439 scopus 로고    scopus 로고
    • Prediction of whole-genome DNA-DNA similarity, determination of G+C content and phylogenetic analysis within the family Pasteurellaceae by multilocus sequence analysis (MLSA)
    • Kuhnert P., Korczak B.M. Prediction of whole-genome DNA-DNA similarity, determination of G+C content and phylogenetic analysis within the family Pasteurellaceae by multilocus sequence analysis (MLSA). Microbiology 2006, 152:2537-2548.
    • (2006) Microbiology , vol.152 , pp. 2537-2548
    • Kuhnert, P.1    Korczak, B.M.2
  • 16
    • 73649209034 scopus 로고
    • Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature
    • Marmur J., Doty P. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J. Mol. Biol. 1962, 5:109-118.
    • (1962) J. Mol. Biol. , vol.5 , pp. 109-118
    • Marmur, J.1    Doty, P.2
  • 17
    • 77958507828 scopus 로고    scopus 로고
    • Functional convergence in reduced genomes of bacterial symbionts spanning 200My of evolution
    • McCutcheon J.P., Moran N.A. Functional convergence in reduced genomes of bacterial symbionts spanning 200My of evolution. Genome Biol. Evol. 2010, 2:708-718.
    • (2010) Genome Biol. Evol. , vol.2 , pp. 708-718
    • McCutcheon, J.P.1    Moran, N.A.2
  • 18
    • 84890634795 scopus 로고    scopus 로고
    • Taxonomic use of the G+C content and DNA:DNA hybridization in the genomic age
    • Meier-Kolthoff J.P., Klenk H.P., Goker M. Taxonomic use of the G+C content and DNA:DNA hybridization in the genomic age. Int. J. Syst. Evol. Microbiol. 2014, 64:352-356.
    • (2014) Int. J. Syst. Evol. Microbiol. , vol.64 , pp. 352-356
    • Meier-Kolthoff, J.P.1    Klenk, H.P.2    Goker, M.3
  • 19
    • 0000198211 scopus 로고
    • Precise measurement of the G+C content of deoxyribonucleic-acid by high-performance liquid-chromatography
    • Mesbah M., Premachandran U., Whitman W.B. Precise measurement of the G+C content of deoxyribonucleic-acid by high-performance liquid-chromatography. Int. J. Syst. Bacteriol. 1989, 39:159-167.
    • (1989) Int. J. Syst. Bacteriol. , vol.39 , pp. 159-167
    • Mesbah, M.1    Premachandran, U.2    Whitman, W.B.3
  • 21
    • 84875897318 scopus 로고    scopus 로고
    • Comparative analyses of base compositions, DNA sizes, and dinucleotide frequency profiles in archaeal and bacterial chromosomes and plasmids
    • Nishida H. Comparative analyses of base compositions, DNA sizes, and dinucleotide frequency profiles in archaeal and bacterial chromosomes and plasmids. Int. J. Evol. Biol. 2012, 2012:342482.
    • (2012) Int. J. Evol. Biol. , vol.2012 , pp. 342482
    • Nishida, H.1
  • 23
    • 73149098333 scopus 로고    scopus 로고
    • Shifting the genomic gold standard for the prokaryotic species definition
    • Richter M., Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:19126-19131.
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 19126-19131
    • Richter, M.1    Rossello-Mora, R.2
  • 24
    • 0036606915 scopus 로고    scopus 로고
    • Base composition bias might result from competition for metabolic resources
    • Rocha E.P.C., Danchin A. Base composition bias might result from competition for metabolic resources. Trends Genet. 2002, 18:291-294.
    • (2002) Trends Genet. , vol.18 , pp. 291-294
    • Rocha, E.P.C.1    Danchin, A.2
  • 26
    • 0011933622 scopus 로고
    • Determination of the base composition of deoxyribonucleic acid from its buoyant density in CsCl
    • Schildkraut C.L., Marmur J., Doty P. Determination of the base composition of deoxyribonucleic acid from its buoyant density in CsCl. J. Mol. Biol. 1962, 4:430-443.
    • (1962) J. Mol. Biol. , vol.4 , pp. 430-443
    • Schildkraut, C.L.1    Marmur, J.2    Doty, P.3
  • 27
    • 70449701463 scopus 로고    scopus 로고
    • Classification of Bacteria and Archaea: past, present and future
    • Schleifer K.H. Classification of Bacteria and Archaea: past, present and future. Syst. Appl. Microbiol. 2009, 32:533-542.
    • (2009) Syst. Appl. Microbiol. , vol.32 , pp. 533-542
    • Schleifer, K.H.1
  • 28
    • 0023991945 scopus 로고
    • Directional mutation pressure and neutral molecular evolution
    • Sueoka N. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. U. S. A. 1988, 85:2653-2657.
    • (1988) Proc. Natl. Acad. Sci. U. S. A. , vol.85 , pp. 2653-2657
    • Sueoka, N.1
  • 29
    • 47749126600 scopus 로고    scopus 로고
    • The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria
    • Thomas S.H., Wagner R.D., Arakaki A.K., Skolnick J., Kirby J.R., Shimkets L.J., Sanford R.A., Löffler F.E. The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria. PLoS ONE 2008, 3:e2103.
    • (2008) PLoS ONE , vol.3 , pp. e2103
    • Thomas, S.H.1    Wagner, R.D.2    Arakaki, A.K.3    Skolnick, J.4    Kirby, J.R.5    Shimkets, L.J.6    Sanford, R.A.7    Löffler, F.E.8
  • 33
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino D.R., Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18:821-829.
    • (2008) Genome Res. , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.