Microbial population structures in the deep marine biosphere, Science, vol.318, pp.97-100, 2007. ,
Microbial diversity in the deep sea and the underexplored ''rare biosphere, Proc. Natl Acad. Sci, vol.103, pp.12115-12120, 2006. ,
Unveiling new microbial eukaryotes in the surface ocean, Curr. Opin. Microbiol, vol.11, pp.213-218, 2008. ,
Second-generation environmental sequencing unmasks marine metazoan biodiversity, Nat. Commun, vol.1, p.98, 2010. ,
Genome sequencing in microfabricated high-density picolitre reactors, Nature, vol.437, pp.376-380, 2005. ,
,
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons, Genome Res, vol.21, pp.494-504, 2011. ,
Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates, Environ. Microbiol, vol.12, pp.118-123, 2009. ,
Removing noise from pyrosequenced amplicons, BMC Bioinformatics, vol.12, p.38, 2011. ,
Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises, Mol. Ecol, vol.19, pp.4-20, 2010. ,
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. ,
Eukaryotic richness in the abyss: insights from pyrotag sequencing, PLoS ONE, vol.6, p.18169, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00604768
Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity, Mol. Ecol. Resources, vol.9, pp.1439-1450, 2009. ,
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments, Bioinformatics, vol.20, pp.2317-2319, 2004. ,
Accurate determination of microbial diversity from 454 pyrosequencing data, Nat. Methods, vol.6, pp.639-641, 2009. ,
The 'rare biosphere': a reality check, Nat. Methods, vol.6, pp.636-637, 2009. ,
Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis, FEMS Microbiol. Rev, vol.21, pp.213-229, 1997. ,
New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras, Appl. Environ. Microbiol, vol.72, pp.5734-5741, 2006. ,
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. ,
Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning, Appl. Environ. Microbiol, vol.67, pp.880-887, 2001. ,
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. ,
Experimental factors affecting PCR-based estimates of microbial species richness and evenness, ISME J, vol.4, pp.642-647, 2010. ,
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. ,
Evaluating putative chimeric sequences from PCR-amplified products, Bioinformatics, vol.21, pp.333-337, 2005. ,
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. ,
Reducing chimera formation during PCR amplification to ensure accurate genotyping, Gene, vol.469, pp.45-51, 2010. ,
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. ,
An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa, Mol. Phylogenet. Evol, vol.42, pp.622-636, 2007. ,
MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0, Mol. Biol. Evol, vol.24, pp.1596-1599, 2007. ,
DESS: a versatile solution for preserving morphology and extractable DNA of nematodes, Nematology, vol.8, pp.367-376, 2006. ,
A molecular evolutionary framework for the phylum Nematoda, Nature, vol.392, pp.71-75, 1998. ,
Accuracy and quality of massively parallel DNA pyrosequencing, Genome Biol, vol.8, p.143, 2007. ,
UNAFold: software for nucleic acid folding and hybridization, Methods Mol. Biol, vol.453, pp.3-31, 2008. ,
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. ,
VEGAN, a package of R functions for community ecology, J. Veg. Sci, vol.14, pp.927-930, 2003. ,
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. ,
Defining operational taxonomic units using DNA barcode data, Philos. Trans. R. Soc. Lond., B. Biol. Sci, vol.360, pp.1935-1943, 2005. ,
Second-generation sequencing derived insights into the temporal biodiversity dynamics of freshwater protists, Mol. Ecol, vol.19, pp.2829-2831, 2010. ,
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. ,
Factors affecting thermodynamic stabilities of RNA 3 x 3 internal loops, Biochemistry, vol.43, pp.12865-12876, 2004. ,
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. ,
Fluorescence-based method for measuring and determining the mechanisms of recombination in quantitative PCR, Clin. Chim. Acta, vol.304, pp.19-28, 2001. ,
Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.), Mol. Biol. Evol, vol.16, pp.491-501, 1999. ,
Nematode-specific PCR primers for the 18S small subunit rRNA gene, Mol. Ecol. Notes, vol.5, pp.611-612, 2005. ,
,
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. ,
Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases, Int. J. Syst. Evol. Microbiol, vol.53, pp.289-293, 2003. ,
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. ,
Stimulation and suppression of PCR-mediated recombination, Nucleic Acids Res, vol.26, pp.1819-1825, 1998. ,
DNA recombination during PCR, Nucleic Acids Res, vol.18, pp.1687-1691, 1990. ,
Field guide to next-generation DNA sequencers, Mol. Ecol. Resources, vol.11, pp.759-769, 2011. ,
DNA sequencing with chain-terminating inhibitors, Proc. Natl Acad. Sci. USA, vol.74, pp.5463-5467, 1977. ,
The evolutionary significance of parasitism: do parasite-driven genetic dynamics occur ex silico?, J. Evol. Biol, vol.15, pp.1-9, 2002. ,
Rapid evolution in plant chitinases: Molecular targets of selection in plant-pathogen coevolution, Proc. Natl Acad. Sci. USA, vol.97, pp.5322-5327, 2000. ,
Massive parallel MHC genotyping: titanium that shines, Mol. Ecol, vol.18, pp.1818-1820, 2009. ,
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. ,
Toxicity in animals Trends in evolution?, Toxicon, vol.39, pp.87-96, 2001. ,