Insect-Specific Polyketide Synthases (PKSs), Potential PKS-Nonribosomal Peptide Synthetase Hybrids, and Novel PKS Clades in Tropical Fungi, Applied and Environmental Microbiology, vol.75, issue.11, pp.3721-3732, 2009. ,
DOI : 10.1128/AEM.02744-08
Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics, Mol Ecol, 2015. ,
Exploration of community traits as ecological markers in microbial metagenomes, Molecular Ecology, vol.38, issue.8, pp.1909-1917, 2012. ,
DOI : 10.1093/nar/gkq066
Arthropod Diversity in a Tropical Forest, Science, vol.3148, issue.14, pp.1481-1484, 2012. ,
DOI : 10.1146/annurev.en.25.010180.001025
URL : https://hal.archives-ouvertes.fr/hal-00817285
GenBank, Nucleic Acids Research, vol.41, issue.D1, pp.36-42, 2013. ,
DOI : 10.1093/nar/gks1195
URL : https://academic.oup.com/nar/article-pdf/30/1/17/9901024/300017.pdf
Accurate whole human genome sequencing using reversible terminator chemistry, Nature, vol.34, issue.7218, pp.53-59, 2008. ,
DOI : 10.1101/gr.8.3.175
URL : http://doi.org/10.1038/nature07517
Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke, New Phytologist, vol.18, issue.3, pp.1021-1030, 2014. ,
DOI : 10.1101/gr.074492.107
Wide distribution of related satellite DNA families within the genus Pimelia (Tenebrionidae), 2007. ,
Transcriptome and full-length cDNA resources for the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major insect pest of pine forests, Insect Biochem Mol Biol, vol.42, pp.525-536, 2012. ,
Genomics-driven discovery of the pneumocandin biosynthetic gene cluster in the fungus Glarea lozoyensis, BMC Genomics, vol.14, issue.1, p.339, 2013. ,
DOI : 10.1038/sj.jim.7000115
Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample, Molecular Biology and Evolution, vol.32, issue.9, 2015. ,
DOI : 10.1093/molbev/msv111
Arthropods and inherited bacteria: from counting the symbionts to understanding how symbionts count, BMC Biology, vol.11, issue.1, p.45, 2013. ,
DOI : 10.1098/rsbl.2012.0144
URL : http://doi.org/10.1186/1741-7007-11-45
Bacterial symbionts in insects or the story of communities affecting communities, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.326, issue.5949, pp.1389-1400, 2011. ,
DOI : 10.1126/science.1177531
URL : https://hal.archives-ouvertes.fr/hal-00784710
Species detection using environmental DNA from water samples, Biology Letters, vol.317, issue.5834, pp.423-425, 2008. ,
DOI : 10.1126/science.1141758
URL : https://hal.archives-ouvertes.fr/halsde-00308650
Chemosensory proteins in the honey bee: Insights from the annotated genome, comparative analyses and expressional profiling, Insect Biochemistry and Molecular Biology, vol.37, issue.1, pp.19-28, 2007. ,
DOI : 10.1016/j.ibmb.2006.09.009
Insect symbionts as hidden players in insect???plant interactions, Trends in Ecology & Evolution, vol.27, issue.12, pp.705-711, 2012. ,
DOI : 10.1016/j.tree.2012.08.013
Sequence and phylogenetic analysis of the complete mitochondrial genome of the flour beetle Tribolium castanaeum, Molecular Phylogenetics and Evolution, vol.26, issue.3, pp.502-512, 2003. ,
DOI : 10.1016/S1055-7903(02)00335-4
Bulk De Novo Mitogenome Assembly from Pooled Total DNA Elucidates the Phylogeny of Weevils (Coleoptera: Curculionoidea), Molecular Biology and Evolution, vol.31, issue.8, pp.2223-2237, 2014. ,
DOI : 10.1093/molbev/msu154
Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages, Methods Ecol Evol, 2015. ,
APPLICATION OF INTER???SIMPLE SEQUENCE REPEATS TO INSECT CELL LINES: IDENTIFICATION AT THE CLONAL AND TISSUE-SPECIFIC LEVEL*, In Vitro Cellular & Developmental Biology - Animal, vol.20, issue.8, pp.353-363, 2003. ,
DOI : 10.1290/1543-706X(2003)039<0353:AOISRT>2.0.CO;2
A quick guide to large-scale genomic data mining:e1000779. i5K Consortium. 2013. The i5K initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment, PLoS Comput Biol, vol.6, 2010. ,
DOI : 10.1371/journal.pcbi.1000779
URL : https://doi.org/10.1371/journal.pcbi.1000779
Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding, Ecology Letters, vol.2, issue.10, pp.1245-1257, 2013. ,
DOI : 10.1186/2047-217X-2-4
Repbase Update, a database of eukaryotic repetitive elements, Cytogenetic and Genome Research, vol.5, issue.1-4, pp.462-467, 2005. ,
DOI : 10.1016/S1360-1385(02)02372-5
MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Research, vol.33, issue.2, pp.511-518, 2005. ,
DOI : 10.1093/nar/gki198
Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest, Genome Biology, vol.14, issue.3, p.27, 2013. ,
DOI : 10.1093/nar/gkr201
Bioprospecting Potential of the Soil Metagenome: Novel Enzymes and Bioactivities, Genomics & Informatics, vol.11, issue.3, pp.114-120, 2013. ,
DOI : 10.5808/GI.2013.11.3.114
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics, Nucleic Acids Research, vol.40, issue.W1, pp.622-627, 2012. ,
DOI : 10.1093/nar/gks540
URL : https://academic.oup.com/nar/article-pdf/40/W1/W622/4932016/gks540.pdf
Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family, Molecular Ecology Resources, vol.65, pp.966-975, 2014. ,
DOI : 10.1016/j.ympev.2012.07.015
CDD: a Conserved Domain Database for the functional annotation of proteins, Nucleic Acids Research, vol.39, issue.Database, pp.225-229, 2011. ,
DOI : 10.1093/nar/gkq1189
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods, Nature Methods, vol.22, issue.6, pp.495-500, 2007. ,
DOI : 10.1093/oxfordjournals.molbev.a026048
Tropical Arthropod Species, More or Less?, Science, vol.416, issue.6883, pp.41-42, 2010. ,
DOI : 10.1038/416841a
Stable Introduction of a Life-Shortening Wolbachia Infection into the Mosquito Aedes aegypti, Science, vol.5, issue.5, pp.141-144, 2009. ,
DOI : 10.1038/nrmicro1638
Sequencing technologies ??? the next generation, Nature Reviews Genetics, vol.37, issue.1, pp.31-46, 2010. ,
DOI : 10.1016/j.tig.2007.12.006
Assembly algorithms for next-generation sequencing data, Genomics, vol.95, issue.6, pp.315-327, 2010. ,
DOI : 10.1016/j.ygeno.2010.03.001
URL : https://doi.org/10.1016/j.ygeno.2010.03.001
Phylogenomics resolves the timing and pattern of insect evolution, Science, vol.19, issue.4, pp.763-767, 2014. ,
DOI : 10.1093/aesa/19.4.440
Horizontal gene transfers in insects, Current Opinion in Insect Science, vol.7, pp.24-29, 2015. ,
DOI : 10.1016/j.cois.2015.03.006
Unipro UGENE: a unified bioinformatics toolkit, Bioinformatics, vol.28, issue.8, pp.1166-1167, 2012. ,
DOI : 10.1093/bioinformatics/bts091
URL : https://academic.oup.com/bioinformatics/article-pdf/28/8/1166/18531177/bts091.pdf
Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics, Molecular Ecology Resources, vol.11, issue.Suppl 1, 2014. ,
DOI : 10.1111/j.1755-0998.2010.02920.x
A DESCRIPTIVE FRAMEWORK FOR THE FIELD OF DATA MINING AND KNOWLEDGE DISCOVERY, International Journal of Information Technology & Decision Making, vol.4, issue.04, pp.639-682, 2008. ,
DOI : 10.1145/360402.360406
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Research, vol.41, issue.D1, pp.590-596, 2013. ,
DOI : 10.1093/nar/gks1219
URL : https://academic.oup.com/nar/article-pdf/41/D1/D590/3690367/gks1219.pdf
Algal Biogeography: Metagenomics Shows Distribution of a Picoplanktonic Pelagophyte, Current Biology, vol.22, issue.17, pp.682-683, 2012. ,
DOI : 10.1016/j.cub.2012.07.030
Histone and ribosomal RNA repetitive gene clusters of the boll weevil are linked in a tandem array, Insect Molecular Biology, vol.31, pp.463-471, 2010. ,
DOI : 10.1093/aesa/91.6.771
Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics, American Journal of Botany, vol.99, issue.2, pp.349-364, 2012. ,
DOI : 10.3732/ajb.1100335
DNA Fingerprinting, DNA Barcoding, and Next Generation Sequencing Technology in Plants, Methods Mol Biol, vol.862, pp.13-22, 2012. ,
DOI : 10.1007/978-1-61779-609-8_2
Environmental DNA, Molecular Ecology, vol.21, issue.8, pp.1789-1793, 2012. ,
DOI : 10.1111/j.1365-294X.2011.05362.x
URL : https://hal.archives-ouvertes.fr/insu-00845082
Towards next-generation biodiversity assessment using DNA metabarcoding, Molecular Ecology, vol.317, issue.8, pp.2045-2050, 2012. ,
DOI : 10.1111/j.1365-294X.2012.05545.x
Multiplex sequencing of pooled mitochondrial genomes???a crucial step toward biodiversity analysis using mito-metagenomics, Nucleic Acids Research, vol.42, issue.22, p.166, 2014. ,
DOI : 10.1093/nar/gku917
Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences, Curr Protoc Bioinformatics. Chapter, vol.1, 2009. ,
DOI : 10.1371/journal.pbio.0000045
Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction, Trends in Microbiology, vol.21, issue.12, pp.641-651, 2013. ,
DOI : 10.1016/j.tim.2013.09.005
L approach, Molecular Ecology Resources, vol.7, issue.1, pp.51-60, 2009. ,
DOI : 10.1111/j.1755-0998.2008.02352.x
The effect of plant identity and the level of plant decay on molecular gut content analysis in a herbivorous soil insect, Molecular Ecology Resources, vol.169, issue.1, pp.75-83, 2013. ,
DOI : 10.1007/s00442-011-2210-y
(Apocynaceae), PeerJ, vol.120, p.718, 2015. ,
DOI : 10.7717/peerj.718/supp-6
Wolbachia: master manipulators of invertebrate biology, Nature Reviews Microbiology, vol.12, issue.10, pp.741-751, 2008. ,
DOI : 10.1099/ijs.0.64515-0
The Biology of the Coleoptera., Systematic Zoology, vol.31, issue.3, pp.342-345, 1982. ,
DOI : 10.2307/2413243
Dfam: a database of repetitive DNA based on profile hidden Markov models, D1): D70-D82 first published online, pp.10-1093, 2012. ,
DOI : 10.1093/nar/gks1265
A unified classification system for eukaryotic transposable elements, Nature Reviews Genetics, vol.8, issue.12, pp.973-982, 2007. ,
DOI : 10.1101/SQB.1984.049.01.039
URL : https://hal.archives-ouvertes.fr/hal-00169819
Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence, Nature Reviews Genetics, vol.5, pp.59-69, 2012. ,
DOI : 10.1186/gb-2004-5-9-r61
The microbial gene diversity along an elevation gradient of the Tibetan grassland, The ISME Journal, vol.105, issue.2, pp.1-11, 2013. ,
DOI : 10.1073/pnas.0709016105
The future of environmental DNA in ecology, Molecular Ecology, vol.25, issue.8, pp.2031-2038, 2012. ,
DOI : 10.1111/j.1365-294X.2012.05545.x
Beyond the genome: community-level analysis of the microbial world, Biology & Philosophy, vol.24, issue.2, pp.261-282, 2013. ,
DOI : 10.1038/nbt1214
Animal biodiversity: an introduction to higher-level classification and taxonomic richness, Zootaxa, vol.12, pp.7-12, 2011. ,
Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification, GigaScience, vol.2, issue.1, 2013. ,
DOI : 10.1186/2047-217X-2-4