Encyclopedia of Metagenomics

2015 Edition
| Editors: Karen E. Nelson

Evaluating Putative Chimeric Sequences from PCR-Amplified Products

  • Juan M. Gonzalez
Reference work entry
DOI: https://doi.org/10.1007/978-1-4899-7478-5_791

Introduction

The term chimera has its origins in the Greek mythology defining a creature composed of body parts from different living beings. In molecular biology, a chimeric sequence or chimera is a DNA sequence composed of DNA fragments originated from two or more genes or genomes.

Chimeric sequences can be naturally generated during DNA recombination which occurs naturally within a genome or by taking up foreign DNA by an organism. These processes of crossover recombination are of interest in phylogenetic and evolution studies and need to be identified (Posada and Crandall 2002). Nevertheless, chimeras represent a serious problem to be considered when they are generated as artifacts during DNA manipulation and/or analysis.

Chimeric artifacts can be produced at different stages during experimental DNA studies. Some examples can be described relating to cloning procedures, DNA amplification, and/or DNA assembling during computational analysis (Fig. 1).
This is a preview of subscription content, log in to check access.

Notes

Acknowledgments

The author acknowledges funding from the Spanish Ministry of Economy and Competitiveness, project CONSOLIDER CSD2009-00006, which includes participation of Feder funds.

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.PubMedCrossRefGoogle Scholar
  2. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ. At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol. 2005;71:7724–36.PubMedCentralPubMedCrossRefGoogle Scholar
  3. Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.PubMedCentralPubMedCrossRefGoogle Scholar
  4. Cole JR, Chai B, Marsh TL, et al. The Ribosomal Database Project (RDPII): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucl Acids Res. 2003;31:442–3.PubMedCentralPubMedCrossRefGoogle Scholar
  5. Cole JR, Wang Q, Cardenas E, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucl Acids Res. 2009;37:D141–5.PubMedCentralPubMedCrossRefGoogle Scholar
  6. Curtis TP, Sloan WT, Scannell JW. Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA. 2002;99:10494–9.PubMedCentralPubMedCrossRefGoogle Scholar
  7. DeSantis TZ, Hugenholtz P, Larsen N, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72:5069–72.PubMedCentralPubMedCrossRefGoogle Scholar
  8. Edgar RC, Haas BJ, Clemente JC, et al. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27:2194–200.PubMedCentralPubMedCrossRefGoogle Scholar
  9. Gonzalez JM, Zimmermann J, Saiz-Jimenez C. Evaluating putative chimeric sequences from PCR-amplified products. Bioinformatics. 2005;21:333–7.PubMedCrossRefGoogle Scholar
  10. Gonzalez JM, Portillo MC, Belda-Ferre P, Mira A. Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities. PLoS ONE. 2012;7(1):e29973.PubMedCentralPubMedCrossRefGoogle Scholar
  11. Haas BJ, Gevers D, Earl AM, et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 2011;21:494–504.PubMedCentralPubMedCrossRefGoogle Scholar
  12. Hugenholtz P, Huber T. Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Intl J Syst Evol Microbiol. 2003;53:289–93.CrossRefGoogle Scholar
  13. Mende DR, Waller AS, Sunagawa S, et al. Assessment of metagenomic assembly using simulated next generation sequencing data. PLoS ONE. 2012;7(2):e31386.PubMedCentralPubMedCrossRefGoogle Scholar
  14. Posada D, Crandall AK. The effect of recombination on the accuracy of phylogeny estimation. J Mol Evol. 2002;54:396–402.PubMedCrossRefGoogle Scholar
  15. Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl Acids Res. 2013;41:D590–6.PubMedCentralPubMedCrossRefGoogle Scholar
  16. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ. Removing noise from pyrosequenced amplicons. BMC Bioinforma. 2011;12:38.CrossRefGoogle Scholar
  17. Roesch LFW, Fulthorpe RR, Riva A, et al. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 2007;1:283–90.PubMedCentralPubMedGoogle Scholar
  18. Sambrook JJ, Russell DDW. Molecular cloning. A laboratory manual. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 2001.Google Scholar
  19. Schloss PD, Westcott SL, Ryabin T, et al. Introducing mother: open-source, platform-independent, community supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–41.PubMedCentralPubMedCrossRefGoogle Scholar
  20. Wintzingerode F, Göbel UB, Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-base rRNA analysis. FEMS Microbiol Rev. 1997;21:213–29.CrossRefGoogle Scholar
  21. Wright ES, Yilmaz LS, Noguera DR. DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol. 2011;78:717–25.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSICSevilleSpain