S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

D. Altshuler, R. Durbin, G. Abecasis, D. Bentley, A. Chakravarti et al., A map of human genome variation from population-scale sequencing, Nature, vol.467, issue.7319, pp.1061-1073, 2010.

A. Bankevich, S. Nurk, D. Antipov, A. Gurevich, M. Dvorkin et al., SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing, Journal of Computational Biology, vol.19, issue.5, pp.455-477, 2012.
DOI : 10.1089/cmb.2012.0021

J. Besemer, A. Lomsadze, and M. Borodovsky, GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions, Nucleic Acids Research, vol.29, issue.12, pp.2607-2618, 2001.
DOI : 10.1093/nar/29.12.2607

M. Depristo, E. Banks, R. Poplin, K. Garimella, J. Maguire et al., A framework for variation discovery and genotyping using next-generation DNA sequencing data, Nature Genetics, vol.8, issue.5, pp.491-498, 2011.
DOI : 10.1126/science.1177074

J. Ferrari, J. West, S. Via, and H. Godfray, POPULATION GENETIC STRUCTURE AND SECONDARY SYMBIONTS IN HOST-ASSOCIATED POPULATIONS OF THE PEA APHID COMPLEX, Evolution, vol.21, issue.2, pp.375-390, 2012.
DOI : 10.1111/j.1558-5646.2011.01436.x

T. Fukatsu, T. Tsuchida, N. Nikoh, and R. Koga, Spiroplasma Symbiont of the Pea Aphid, Acyrthosiphon pisum (Insecta: Homoptera), Applied and Environmental Microbiology, vol.67, issue.3, pp.1284-1291, 2001.
DOI : 10.1128/AEM.67.3.1284-1291.2001

R. Handsaker, J. Korn, J. Nemesh, and S. Mccarroll, Discovery and genotyping of genome structural polymorphism by sequencing on a population scale, Nature Genetics, vol.467, issue.3, pp.269-276, 2011.
DOI : 10.1101/gr.078212.108

L. Henry, J. Peccoud, J. Simon, J. Hadfield, M. Maiden et al., Horizontally Transmitted Symbionts and Host Colonization of Ecological Niches, Current Biology, vol.23, issue.17, pp.1713-1717, 2013.
DOI : 10.1016/j.cub.2013.07.029

A. Kostic, A. Ojesina, C. Pedamallu, J. Jung, R. Verhaak et al., PathSeq: software to identify or discover microbes by deep sequencing of human tissue, Nature Biotechnology, vol.29, issue.5, pp.4-7, 2011.
DOI : 10.1038/nmeth.1451

S. Kurtz, A. Phillippy, A. Delcher, M. Smoot, M. Shumway et al., Versatile and open software for comparing large genomes, 2004.

B. Langmead and S. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-354, 2012.
DOI : 10.1093/bioinformatics/btp352
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322381

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-60, 2009.
DOI : 10.1093/bioinformatics/btp324

F. Legeai, S. Shigenobu, J. Gauthier, J. Colbourne, C. Rispe et al., AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome, Insect Molecular Biology, vol.21, issue.1, pp.5-12, 2010.
DOI : 10.1111/j.1365-2583.2009.00930.x
URL : https://hal.archives-ouvertes.fr/inria-00531562

G. Lunter and M. Goodson, Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads, Genome Research, vol.21, issue.6, pp.936-939, 2011.
DOI : 10.1101/gr.111120.110

T. Magoc, S. Pabinger, S. Canzar, X. Liu, Q. Su et al., GAGE-B: an evaluation of genome assemblers for bacterial organisms, Bioinformatics, vol.29, issue.14, pp.1718-1725, 2013.
DOI : 10.1093/bioinformatics/btt273

A. Mclean, M. Van-asch, J. Ferrari, and H. Godfray, Effects of bacterial secondary symbionts on host plant use in pea aphids, Proceedings of the Royal Society B: Biological Sciences, vol.55, issue.12, pp.760-766, 1706.
DOI : 10.1146/annurev-ento-112408-085305

R. Nielsen, J. Paul, A. Albrechtsen, and Y. Song, Genotype and SNP calling from next-generation sequencing data, Nature Reviews Genetics, vol.25, issue.6, pp.443-451, 2011.
DOI : 10.1038/nrg2986

K. Oliver, P. Degnan, G. Burke, and N. Moran, Facultative Symbionts in Aphids and the Horizontal Transfer of Ecologically Important Traits, Annual Review of Entomology, vol.55, issue.1, pp.247-266, 2010.
DOI : 10.1146/annurev-ento-112408-085305

J. Peccoud, A. Ollivier, M. Plantegenest, and J. Simon, A continuum of genetic divergence from sympatric host races to species in the pea aphid complex, Proceedings of the National Academy of Sciences, vol.106, issue.18, pp.7495-7500, 2009.
DOI : 10.1073/pnas.0811117106
URL : https://hal.archives-ouvertes.fr/hal-00729934

J. Peccoud, J. Simon, H. Mclaughlin, and N. Moran, Post-Pleistocene radiation of the pea aphid complex revealed by rapidly evolving endosymbionts, Proceedings of the National Academy of Sciences, vol.106, issue.38, pp.16315-16320, 2009.
DOI : 10.1073/pnas.0905129106

G. Rizk, D. Lavenier, and R. Chikhi, DSK: k-mer counting with very low memory usage, Bioinformatics, vol.29, issue.5, pp.652-655, 2013.
DOI : 10.1093/bioinformatics/btt020
URL : https://hal.archives-ouvertes.fr/hal-00778473

R. Schmieder and R. Edwards, Quality control and preprocessing of metagenomic datasets, Bioinformatics, vol.27, issue.6, pp.863-864, 2011.
DOI : 10.1093/bioinformatics/btr026

J. Simon, S. Carré, M. Boutin, ?. Prunier, N. Leterme et al., Host-based divergence in populations of the pea aphid: insights from nuclear markers and the prevalence of facultative symbionts, Proceedings of the Royal Society B: Biological Sciences, vol.270, issue.1525, pp.1703-1712, 1525.
DOI : 10.1098/rspb.2003.2430

V. Sousa and J. Hey, Understanding the origin of species with genome-scale data: modelling gene flow, Nature Reviews Genetics, vol.154, issue.6, pp.404-414, 2013.
DOI : 10.1093/bioinformatics/18.2.337

T. Tsuchida, R. Koga, and T. Fukatsu, Host plant specialization governed 730 by facultative symbiont, Science, vol.303, 1989.

S. Via, Specialized Host Plant Performance of Pea Aphid Clones is not Altered by Experience, Ecology, vol.72, issue.4, pp.1420-1427, 1991.
DOI : 10.2307/1941114