. Insa-lyon, . Bf2i, B. Inra, ;. Fonctionnelle, . Cnrs-umr5557-ecologie et al., Insectes et Interactions, Bât. Louis Pasteur 20 ave. Albert Einstein, F-69621 Villeurbanne, BMC Genomics, vol.11, issue.2, 2010.

I. Microbienne and F. Villeurbanne,

J. Dale, Molecular Genetics of Bacteria, 2004.

B. J. Peter, J. Arsuaga, A. M. Breier, A. B. Khodursky, P. O. Brown et al., Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli, Genome Biol, vol.5, p.87, 2004.

R. Sorek and P. Cossart, Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity, Nat Rev Genet, vol.11, pp.9-16, 2010.

M. D. Prickett, M. Page, A. E. Douglas, and G. H. Thomas, BuchneraBASE: a postgenomic resource for Buchnera sp, APS. Bioinformatics, vol.22, pp.641-642, 2006.

N. A. Moran, M. A. Munson, P. Baumann, and H. Ishikawa, A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts, Proceedings of the Royal Society of London, Series B Biological Sciences, vol.253, pp.167-171, 1993.

M. A. Munson, P. Baumann, M. A. Clark, L. Baumann, N. A. Moran et al., Evidence for the establishment of aphid-eubacterium endosymbiosis in an ancestor of four aphid families, Journal of Bacteriology, vol.173, pp.6321-6324, 1991.

R. Gil, A. Latorre, and A. Moya, Bacterial endosymbionts of insects: insights from comparative genomics, Environmental microbiology, vol.6, pp.1109-1122, 2004.

N. A. Moran, Accelerated evolution and Muller's rachet in endosymbiotic bacteria, Proceedings of the National Academy of Sciences of the, vol.93, pp.2873-2878, 1996.

J. J. Wernegreen, Genome evolution in bacterial endosymbionts of insects, Nature Reviews Genetics, vol.3, pp.850-861, 2002.

S. Shigenobu, H. Watanabe, M. Hattori, Y. Sakaki, and H. Ishikawa, Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp, Nature, vol.407, pp.81-86, 2000.

J. Bermingham, A. Rabatel, F. Calevro, J. Vinuelas, G. Febvay et al., Impact of host hevelopmental age on the transcriptome of the symbiotic bacterium Buchnera aphidicola in the pea aphid (Acyrthosiphon pisum), Applied and Environmental Microbiology, vol.75, pp.7294-7297, 2009.

N. Reymond, F. Calevro, J. Vinuelas, N. Morin, Y. Rahbe et al., Different levels of transcriptional regulation due to trophic constraints in the reduced genome of Buchnera aphidicola APS, Applied Environmental Microbiology, vol.72, pp.7760-7766, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00391509

M. T. Edwards, S. Rison, N. G. Stoker, and L. Wernisch, A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context, Nucleic Acids Research, vol.33, pp.3253-3262, 2005.

. Biocyc,

. Microbesonline,

P. R. Romero and P. D. Karp, Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases, Bioinformatics, vol.20, pp.709-717, 2004.

P. Dam, V. Olman, K. Harris, Z. Su, and Y. Xu, Operon prediction using both genome-specific and general genomic information, Nucleic Acids Research, vol.35, pp.288-298, 2007.

M. N. Price, K. H. Huang, and E. J. Alm, Arkin AP: A novel method for accurate operon predictions in all sequenced prokaryotes, Nucleic Acids Research, vol.33, pp.880-892, 2005.

D. B. Regulob,

S. Gama-castro, V. Jimenez-jacinto, M. Peralta-gil, A. Santos-zavaleta, M. I. Penaloza-spinola et al., RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation, Nucleic Acids Research, vol.36, pp.120-124, 2008.

H. Salgado, G. Moreno-hagelsieb, T. F. Smith, and J. Collado-vides, Operons in Escherichia coli: genomic analyses and predictions. Proceedings of the National Academy of Sciences of the, vol.97, pp.6652-6657, 2000.

J. Bockhorst, M. Craven, D. Page, J. Shavlik, and J. Glasner, A Bayesian network approach to operon prediction, Bioinformatics, vol.19, pp.1227-1235, 2003.

K. S. Wilson, V. Hippel, and P. H. , Transcription termination at intrinsic terminators: the role of the RNA hairpin, Proceedings of the National Academy of Sciences of the, vol.92, pp.8793-8797, 1995.

C. L. Kingsford, K. Ayanbule, and S. L. Salzberg, Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake, Genome Biology, vol.8, p.22, 2007.

, The Comprehensive R Archive Network)

S. Charaniya, S. Mehra, W. Lian, K. P. Jayapal, G. Karypis et al., Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor, Nucleic Acids Research, vol.35, pp.7222-7236, 2007.

H. Charles and H. Ishikawa, Physical and genetical map of the genome of Buchnera, the primary endosymbiont of the pea aphid Acyrthosiphon pisum, Journal of Molecular Evolution, vol.48, pp.142-150, 1999.

F. Calevro, H. Charles, N. Reymond, V. Dugas, J. P. Cloarec et al., Assessment of 35 mer amino-modified oligonucleotide based microarray with bacterial samples, Journal of Microbiological Methods, vol.57, pp.207-218, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00402180

L. Baumann, P. Baumann, and M. L. Thao, Detection of messenger RNA transcribed from genes encoding enzymes of amino acid biosynthesis in Buchnera aphidicola (Endosymbiont of aphids), Current Microbiology, vol.38, pp.135-136, 1999.

N. A. Moran and A. Mira, The process of genome shrinkage in the obligate symbiont Buchnera aphidicola, Genome Biology, vol.2, pp.1-12, 2001.

F. J. Silva, A. Latorre, and A. Moya, Genome size reduction through multiple events of gene disintegration in Buchnera APS, Trends in Genetics, vol.17, pp.615-618, 2001.

G. Moreno-hagelsieb and J. Collado-vides, A powerful non-homology method for the prediction of operons in prokaryotes, Bioinformatics, vol.18, issue.1, pp.329-336, 2002.

E. V. Koonin, A. R. Mushegian, and K. E. Rudd, Sequencing and analysis of bacterial genomes, Current Biology, vol.6, pp.404-416, 1996.

C. K. Stover, X. Q. Pham, A. L. Erwin, S. D. Mizoguchi, P. Warrener et al., Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen, Nature, vol.406, pp.959-964, 2000.

K. Postle and R. F. Good, A bidirectional rho-independent transcription terminator between the E. coli tonB gene and an opposing gene, Cell, vol.41, pp.577-585, 1985.

H. Charles, D. Mouchiroud, J. Lobry, I. Goncalves, and Y. Rahbé, Gene size reduction in the bacterial aphid endosymbiont, Buchnera. Molecular Biology and Evolution, vol.16, pp.1820-1822, 1999.
URL : https://hal.archives-ouvertes.fr/hal-00402189

M. N. Price, A. P. Arkin, and E. J. Alm, The life-cycle of operons, PLoS Genetics, vol.2, p.96, 2006.

F. J. Silva, A. Latorre, and A. Moya, Why are the genomes of endosymbiotic bacteria so stable?, Trends in Genetics, vol.19, pp.176-180, 2003.

I. Tamas, L. Klasson, B. Canback, A. K. Naslund, A. S. Eriksson et al., Andersson SGE: 50 million years of genomic stasis in endosymbiotic bacteria, Science, vol.296, pp.2376-2379, 2002.

N. A. Moran, H. J. Mclaughlin, and R. Sorek, The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria, Science, vol.323, pp.379-382, 2009.

I. B. Rogozin, K. S. Makarova, D. A. Natale, A. N. Spiridonov, R. L. Tatusov et al., Congruent evolution of different classes of non-coding DNA in prokaryotic genomes, Nucleic Acids Research, vol.30, pp.4264-4271, 2002.

J. Tamames, A. Moya, and A. Valencia, Modular organization in the reductive evolution of protein-protein interaction networks, Genome Biology, vol.8, p.94, 2007.

. Brinza, Structure and dynamics of the operon map of Buchnera aphidicola sp. strain APS, BMC Genomics, vol.11, p.666, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00632959