J. A. Huber, D. B. Mark-welch, H. G. Morrison, S. M. Huse, P. R. Neal et al., Microbial population structures in the deep marine biosphere, Science, vol.318, pp.97-100, 2007.

M. L. Sogin, H. G. Morrison, J. A. Huber, D. Mark-welch, S. M. Huse et al., Microbial diversity in the deep sea and the underexplored ''rare biosphere, Proc. Natl Acad. Sci, vol.103, pp.12115-12120, 2006.

R. Massana and C. Pedros-alio, Unveiling new microbial eukaryotes in the surface ocean, Curr. Opin. Microbiol, vol.11, pp.213-218, 2008.

V. G. Fonseca, G. R. Carvalho, W. Sung, H. F. Johnson, D. M. Power et al., Second-generation environmental sequencing unmasks marine metazoan biodiversity, Nat. Commun, vol.1, p.98, 2010.

M. Margulies, M. Egholm, W. E. Altman, S. Attiya, J. S. Bader et al., Genome sequencing in microfabricated high-density picolitre reactors, Nature, vol.437, pp.376-380, 2005.

B. J. Haas, D. Gevers, A. M. Earl, M. Feldgarden, D. V. Ward et al.,

E. Sodergren, Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons, Genome Res, vol.21, pp.494-504, 2011.

V. Kunin, A. Engelbrektson, H. Ochman, and P. Hugenholtz, Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates, Environ. Microbiol, vol.12, pp.118-123, 2009.

C. Quince, A. Lanzen, R. J. Davenport, and P. J. Turnbaugh, Removing noise from pyrosequenced amplicons, BMC Bioinformatics, vol.12, p.38, 2011.

S. Creer, V. G. Fonseca, D. L. Porazinska, R. M. Giblin-davis, W. Sung et al., Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises, Mol. Ecol, vol.19, pp.4-20, 2010.

E. Pruesse, C. Quast, K. Knittel, B. Fuchs, W. Ludwig et al., SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic Acids Res, vol.35, pp.7188-7196, 2007.

J. Pawlowski, R. Christen, B. Lecroq, D. Bachar, H. R. Shahbazkia et al., Eukaryotic richness in the abyss: insights from pyrotag sequencing, PLoS ONE, vol.6, p.18169, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00604768

D. Porazinska, R. Giblin-davis, L. Faller, W. Farmerie, N. Kanzaki et al., Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity, Mol. Ecol. Resources, vol.9, pp.1439-1450, 2009.

T. Huber, G. Faulkner, and P. Hugenholtz, Bellerophon: a program to detect chimeric sequences in multiple sequence alignments, Bioinformatics, vol.20, pp.2317-2319, 2004.

C. Quince, A. Lanzen, T. P. Curtis, R. J. Davenport, N. Hall et al., Accurate determination of microbial diversity from 454 pyrosequencing data, Nat. Methods, vol.6, pp.639-641, 2009.

J. Reeder and R. Knight, The 'rare biosphere': a reality check, Nat. Methods, vol.6, pp.636-637, 2009.

F. Von-wintzingerode, U. B. Gobel, and E. Stackebrandt, Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis, FEMS Microbiol. Rev, vol.21, pp.213-229, 1997.

K. E. Ashelford, N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J. Weightman, New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras, Appl. Environ. Microbiol, vol.72, pp.5734-5741, 2006.

G. C. Wang and Y. Wang, Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes, Appl. Environ. Microbiol, vol.63, pp.4645-4650, 1997.

X. Qiu, L. Wu, H. Huang, P. E. Mcdonel, A. V. Palumbo et al., Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning, Appl. Environ. Microbiol, vol.67, pp.880-887, 2001.

D. J. Lahr and L. A. Katz, Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase, Biotechniques, vol.47, pp.857-866, 2009.

A. Engelbrektson, V. Kunin, K. C. Wrighton, N. Zvenigorodsky, F. Chen et al., Experimental factors affecting PCR-based estimates of microbial species richness and evenness, ISME J, vol.4, pp.642-647, 2010.

J. R. Cole, B. Chai, T. L. Marsh, R. J. Farris, Q. Wang et al., The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy, Nucleic Acids Res, vol.31, pp.442-443, 2003.

J. M. Gonzalez, J. Zimmermann, and C. Saiz-jimenez, Evaluating putative chimeric sequences from PCR-amplified products, Bioinformatics, vol.21, pp.333-337, 2005.

K. E. Ashelford, N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J. Weightman, At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies, Appl. Environ. Microbiol, vol.71, pp.7724-7736, 2005.

R. P. Smyth, T. E. Schlub, A. Grimm, V. Venturi, A. Chopra et al., Reducing chimera formation during PCR amplification to ensure accurate genotyping, Gene, vol.469, pp.45-51, 2010.

G. C. Wang and Y. Wang, The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species, Microbiology, vol.142, pp.1107-1114, 1996.

B. H. Meldal, N. J. Debenham, P. De-ley, I. T. De-ley, J. R. Vanfleteren et al., An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa, Mol. Phylogenet. Evol, vol.42, pp.622-636, 2007.

K. Tamura, J. Dudley, M. Nei, and S. Kumar, MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0, Mol. Biol. Evol, vol.24, pp.1596-1599, 2007.

M. Yoder, I. T. De-ley, I. W. King, M. Mundo-ocampo, J. Mann et al., DESS: a versatile solution for preserving morphology and extractable DNA of nematodes, Nematology, vol.8, pp.367-376, 2006.

M. L. Blaxter, P. De-ley, J. R. Garey, L. X. Liu, P. Scheldeman et al., A molecular evolutionary framework for the phylum Nematoda, Nature, vol.392, pp.71-75, 1998.

S. M. Huse, J. A. Huber, H. G. Morrison, M. L. Sogin, and D. M. Welch, Accuracy and quality of massively parallel DNA pyrosequencing, Genome Biol, vol.8, p.143, 2007.

N. R. Markham and M. Zuker, UNAFold: software for nucleic acid folding and hybridization, Methods Mol. Biol, vol.453, pp.3-31, 2008.

C. Ricotta and L. Szeidl, Towards a unifying approach to diversity measures: bridging the gap between the Shannon entropy and Rao's quadratic index. Theor, Popul. Biol, vol.70, pp.237-243, 2006.

P. Dixon and M. W. Palmer, VEGAN, a package of R functions for community ecology, J. Veg. Sci, vol.14, pp.927-930, 2003.

P. V. Snelgrove, Getting to the bottom of marine biodiversity: Sedimentary habitats -Ocean bottoms are the most widespread habitat on Earth and support high biodiversity and key ecosystem services, Bioscience, vol.49, pp.129-138, 1999.

M. Blaxter, J. Mann, T. Chapman, F. Thomas, C. Whitton et al., Defining operational taxonomic units using DNA barcode data, Philos. Trans. R. Soc. Lond., B. Biol. Sci, vol.360, pp.1935-1943, 2005.

S. Creer, Second-generation sequencing derived insights into the temporal biodiversity dynamics of freshwater protists, Mol. Ecol, vol.19, pp.2829-2831, 2010.

R. A. Clayton, G. Sutton, P. S. Hinkle, . Jr, C. Bult et al., Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa, Int. J. Syst. Bacteriol, vol.45, pp.595-599, 1995.

G. Chen, B. M. Znosko, X. Jiao, and D. H. Turner, Factors affecting thermodynamic stabilities of RNA 3 x 3 internal loops, Biochemistry, vol.43, pp.12865-12876, 2004.

L. Wu, T. Tang, R. Zhou, and S. Shi, PCR-mediated recombination of the amplification products of the Hibiscus tiliaceus cytosolic glyceraldehyde-3-phosphate dehydrogenase gene, J. Biochem. Mol. Biol, vol.40, pp.172-179, 2007.

F. V. Shammas, R. Heikkila, and A. Osland, Fluorescence-based method for measuring and determining the mechanisms of recombination in quantitative PCR, Clin. Chim. Acta, vol.304, pp.19-28, 2001.

R. L. Small, J. A. Ryburn, and J. F. Wendel, Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.), Mol. Biol. Evol, vol.16, pp.491-501, 1999.

R. M. Floyd, A. D. Rogers, P. J. Lambshead, and C. R. Smith, Nematode-specific PCR primers for the 18S small subunit rRNA gene, Mol. Ecol. Notes, vol.5, pp.611-612, 2005.

P. De-ley, I. T. De-ley, K. Morris, E. Abebe, M. Mundo-ocampo et al.,

A. Olivares, J. Burr, and A. H. , An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding, Philos. Trans. R. Soc. Lond., B. Biol. Sci, vol.360, pp.1945-1958, 2005.

P. Hugenholtzt and T. Huber, Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases, Int. J. Syst. Evol. Microbiol, vol.53, pp.289-293, 2003.

A. Jumpponen, Soil fungal communities underneath willow canopies on a primary successional glacier forefront: rDNA sequence results can be affected by primer selection and chimeric data, Microbiol. Ecol, vol.53, pp.233-246, 2007.

M. S. Judo, A. B. Wedel, and C. Wilson, Stimulation and suppression of PCR-mediated recombination, Nucleic Acids Res, vol.26, pp.1819-1825, 1998.

A. Meyerhans, J. P. Vartanian, and S. Wain-hobson, DNA recombination during PCR, Nucleic Acids Res, vol.18, pp.1687-1691, 1990.

T. C. Glenn, Field guide to next-generation DNA sequencers, Mol. Ecol. Resources, vol.11, pp.759-769, 2011.

F. Sanger, S. Nicklen, and A. R. Coulson, DNA sequencing with chain-terminating inhibitors, Proc. Natl Acad. Sci. USA, vol.74, pp.5463-5467, 1977.

T. J. Little, The evolutionary significance of parasitism: do parasite-driven genetic dynamics occur ex silico?, J. Evol. Biol, vol.15, pp.1-9, 2002.

J. G. Bishop, A. M. Dean, and T. Mitchell-olds, Rapid evolution in plant chitinases: Molecular targets of selection in plant-pathogen coevolution, Proc. Natl Acad. Sci. USA, vol.97, pp.5322-5327, 2000.

K. M. Wegner, Massive parallel MHC genotyping: titanium that shines, Mol. Ecol, vol.18, pp.1818-1820, 2009.

T. F. Duda and S. R. Palumbi, Molecular genetics of ecological diversification: Duplication and rapid evolution of toxin genes of the venomous gastropod Conus, Proc. Natl Acad. Sci. USA, vol.96, pp.6820-6823, 1999.

D. Mebs, Toxicity in animals Trends in evolution?, Toxicon, vol.39, pp.87-96, 2001.