Bioinformatics toolkit
www.cardiff.ac.uk/biosi/research/biosoft/

References

Early recognition of chimeras

  1. Bhavsar, D., Zheng, H. and Drysdale, J. (1994) Chimerism in PCR products from a multigene family. Biochemical and Biophysical Research Communications, 205(1): 944-947.
  2. Brakenhoff, R.H., Schoenmakers, J.G. and Lubsen, N.H. (1991) Chimeric cDNA clones: a novel PCR artifact. Nucleic Acids Research, 19:1949.
  3. Kopczynski, E.D., Bateson, M.M. and Ward, D.M. (1994) Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Applied and Environmental Microbiology, 60:746-748.
  4. Meyerhans, A., Vartanian, J.P. and Wain-Hobson, S. (1990) DNA recombination during PCR. Nucleic Acids Resarch, 18: 1687-1691.
  5. Shuldiner, A.R., Nirula, A. and Roth, J. (1989) Hybrid DNA artifact from PCR of closely related target sequences. Nucleic Acids Research, 17:4409

Evidence of chimeras in public repositories

  1. Ashelford, K.E.,Chuzhanova, N.A., Fry, J.C., Jones, A.J. and Weightman, A.J. (2005) At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Applied and Environmental Microbiology, 71(12): 7724-7736.
  2. Hugenholtz, P., Huber, T. (2003)  Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases.  International Journal of Systematic and Evolutionary Microbiology, 53: 289-293.

Quantifying chimera formation

  1. Speksnijder, A.G.C.L., Kowalchuk, G.A., De Jong, S., Kline, E., Stephen, J.R. and Laanbroek, H.J. (2001) Microvariation Artifacts Introduced by PCR and Cloning of Closely Related 16S rRNA Gene Sequences.  Applied and Environmental Microbiology, 67(1): 469-472.
  2. Wang, G.C.-Y., Wang, Y. (1996)  The frequency of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from different bacterial species.  Microbiology, 142: 1107-1114.
  3. Wang, G.C.-Y., Wang, Y. (1997) Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes.  Applied and Environmental Microbiology, 63(12): 4645-4650.

Evidence of 16S rRNA intragenomic variation

  1. Mylvaganam, S. and Dennis, P.P. (1992) Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic Archaebacterium Haloarcula marismortui.  Genetics, 130: 339-410.
  2. Dennis, P.P., Ziesche, S. and Mylvaganam, S. (1998) Transcription analysis of two disparate rRNA operons in the halophilic Archaeon Haloarchcula marismortui. Journal of Bacteriology, 180(18): 4804-4813.
  3. Boucher, Y., Douady, C.J., Sharma, A.K., Kamekura, M. and Doolittle, W.F. (2004) Intragenomic heterogeneity and intragenomic recombination among haloarchaeal rRNA genes. Journal of Bacteriology, 186(12): 3980-3990.
  4. Wang, Y., Zhang, Z. and Ramanan, N. (1997) The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes. Journal of Bacteriology 179(10): 3270-3276.
  5. Acinas, S.G., Marcelino, L.A., Klepac-Ceraj, V. and Polz, M.F. (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. Journal of Bacteriology, 186(9): 2629-2635.
  6. Yap, W.H., Zhang, Z. and Wang, Y. (1999) Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. Journal of Bacteriology, 181(17): 5201-5209.
  7. Teyssier, C., Marchandin, H., De Buochberg, M.S., Ramuz, M. and Jumas-Bilak, E. (2003) Atypical 16S rRNA gene copies in Ochrobacterum intermedium strains reveal a large genomic rearrangement by recombination between rrn copies. Journal of Bacteriology, 185(9): 2901-2909.

Factors influencing chimera formation

  1. Acinas, S.G., Sarma-Rupavtarm, R., Klepac-Ceraj, V. and Polz, M.F. (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample.  Applied and Environmental Microbiology, 71(12): 8966-8969.
  2. Judo, M.S.B., Wedel, A.B. and Wilson, C. (1998) Stimulation and suppression of PCR-mediated recombination. Nucleic Acids Research, 26(7): 1819-1825.
  3. Kanagawa, T. (2003) Bias and artifacts in multitemplate polymerase chain reactions (PCR).  Journal of Bioscience and Bioengineering, 96(4): 317-323.
  4. Kurata, S.,  Kanagawa, T.,  Magariyama, Y., Takatsu, K., Yamada, K., Yokomaku, T. and Kamagata Y. (2004) Reevalution and reduction of a PCR bias caused by reannealing templates.  Applied and Environmental Microbiology, 70(12): 7545-7549.
  5. Odelberg, S.J., Weiss, R.B., Hata, A. and White, R. (1995)  Template-switching during DNA synthesis by Thermus aquaticus DNA polymerase I. Nucleic Acids Research, 23(11): 2049-2057.
  6. Pääbo, S., Irwin, S.D.M. and Wilson, A.C. (1990) DNA damage promotes jumping between templates during enzymatic amplification.  Journal of Biological Chemistry, 265(8): 4718-4721.
  7. Patel, R., Lin, C., Laney, M., Kurn, N., Rose, S. and Ullman, E.F. (1996) Formation of chimeric DNA primer extension products by template switching onto an annealed downstream oligonucleotide.  Proceedings of the National Academy of Sciences of the United States of America, 93(7): 2969-2974.
  8. Qiu, X., Wu, L., Huang, H., McDonel, P.E., Palumbo, A.V., Tiedje, J.M. and Zhou J. (2001) Evaluation of PCR-Generated Chimeras, Mutations, and Heteroduplexes with 16S rRNA Gene-Based Cloning. Applied and Environmental Microbiology, 67(2): 880-887.
  9. Shafikhani, S. (2002) Factors affecting PCR-mediated recombination.  Environmental Microbiology, 4:482-486.
  10. Wang, G.C.-Y., Wang, Y. (1996)  The frequency of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from different bacterial species.  Microbiology, 142: 1107-1114.
  11. Wang, G.C.-Y., Wang, Y. (1997) Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes.  Applied and Environmental Microbiology, 63(12): 4645-4650.

Methods for detecting chimeras

  1. Ashelford, K.E.,Chuzhanova, N.A., Fry, J.C., Jones, A.J. and Weightman, A.J. (2005) At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Applied and Environmental Microbiology, 71(12): 7724-7736.
  2. Gonzalez, J.M., Zimmerman, J. and Saiz-Jimenez, C. (2005) Evaluating putative chimeric sequences from PCR-amplified products.  Bioinformatics, 21(3): 333-337.
  3. Huber, T., Faulkner, G., Hugenholtz, P. (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.  Bioinformatics, 20: 2317-2319.
  4. Klepac-Ceraj, V., Bahr, M., Crump, B.C., Teske, A.P., Hobbie, J.E. and Polz, M.F. (2004) High overall diversity and dominance of microdiverse relationships in salt marsh sulphate-reducing bacteria. Environmental Microbiology, 6: 686-698.
  5. Komatsoulis, G.A., Waterman, M.S. (1997) A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations.  Applied and Environmental Microbiology, 63(6): 2338-2346.
  6. Robison-Cox, J.F., Bateson, M.M. and Ward, D.M. (1995) Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences. Applied and Environmental Microbiology, 61(4): 1240-1245.

Sources of clone libraries used in examples

  1. O’Sullivan, L.A., Fuller, K.E., Thomas, E.M., Turley, C.M., Fry, C.J. and Weightman, A.J. (2004) Distribution and culturability of the uncultivated ‘AGG58 cluster’ of the Bacteroidetes phylum in aquatic environments. FEMS Microbiology Ecology, 47(3): 359-370.
  2. Walker, J.J., Spear, J.R. and Pace, N.R. (2005) Geobiology of a microbial endolithic community in the Yellowstone geothermal environment.  Nature, 434: 1011-1014.

Public DNA repositories

  1. Benson, D.A., Karsch-Mizrachi, I, Lipman, D.J., Ostell, J. and Wheeler, D.L. (2005) GenBank. Nucleic Acids Research, 33: D34-D38.
  2. Cole, J.R., Chai, B., Farris, R.J., Wang, Q., Kulam, S.A., McGarrell, D.M., Garrity, G.M. and Tiedje, J.M. (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis.  Nucleic Acids Research, 33: D294-D296.
  3. Kanz, C. et al. (2005) The EMBL nucleotide sequence database. Nucleic Acids Research, 33: D29-D33.
  4. Tateno, Y., Saitou, N., Okubo, K., Sugawara, H. and Gojobori, T. (2005) DDBJ in collaboration with mass-sequencing teams on annotation.  Nucleic Acids Research, 33: D25-D28.
  5. Wuyts, J., Perrière, G. and Van de Peer, Y. (2004) The European ribosomal RNA database. Nucleic Acids Research, 32: D101-D103.

Hypervariable regions within the 16S rRNA gene

  1. Neefs, J-M., Van De Peer, Y., Hendriks, L. and De Wachter, R. (1990) Compilation of small ribosdomal subunit RNA sequences.  Nucleic Acids Resarch, 18: 2237-2317.

Evolutionary distance

  1. Jukes, T.H. and Cantor, C.R. (1969) Evolution of protein molecules.  p. 21–132. In H. N. Munro (ed.), Mammalian protein metabolism. Academic Press, New York, N.Y.
  2. Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16: 111-120.
  3. Jin, L. and Nei, M. (1990) Limitations of the evolutionary parsimony method of phylogenetic analysis. Molecular Biology and Evolution, 7(1): 82-102.
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Dr K.E. Ashelford. © 2006, Cardiff University