E. A. Barka, P. Vatsa, L. Sanchez, N. Gaveau-vaillant, C. Jacquard et al., Taxonomy, physiology, and natural products of Actinobacteria, Microbiol Mol Biol Rev, vol.80, pp.1-43, 2016.

O. S. Olanrewaju and O. O. Babalola, Streptomyces: implications and interactions in plant growth promotion, Appl Microbiol Biotechnol, vol.103, pp.1179-1188, 2019.

B. Aigle, S. Lautru, D. Spiteller, J. S. Dickschat, G. L. Challis et al., Genome mining of Streptomyces ambofaciens, J Ind Microbiol Biotechnol, vol.41, pp.251-263, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01475037

R. H. Baltz, Gifted microbes for genome mining and natural product discovery, J Ind Microbiol Biotechnol, vol.44, pp.573-588, 2017.

F. Choulet, B. Aigle, A. Gallois, S. Mangenot, C. Gerbaud et al., Evolution of the terminal regions of the Streptomyces linear chromosome, Mol Biol Evol, vol.23, pp.2361-2369, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00112247

M. Redenbach, H. M. Kieser, D. Denapaite, A. Eichner, J. Cullum et al., A set of ordered cosmids and a detailed genetic and physical map for the 8, 1996.

, Mol Microbiol, vol.21, pp.77-96

X. Tian, Z. Zhang, T. Yang, M. Chen, J. Li et al., Comparative genomics analysis of Streptomyces species reveals their adaptation to the marine environment and their diversity at the genomic level, Front Microbiol, vol.7, 2016.

J. Kim, Y. Kim, Y. Jeong, J. Roe, B. Kim et al., Comparative genomics reveals the core and accessory genomes of Streptomyces species, J Microbiol Biotechnol, vol.25, pp.1599-1605, 2015.

Z. Zhou, J. Gu, Y. Li, and Y. Wang, Genome plasticity and systems evolution in Streptomyces, BMC Bioinformatics, vol.13, 2012.

Y. S. Lin, H. M. Kieser, D. A. Hopwood, and C. W. Chen, The chromosomal DNA of Streptomyces lividans 66 is linear, Mol Microbiol, vol.10, pp.923-933, 1993.

C. H. Huang, Y. S. Lin, Y. L. Yang, S. W. Huang, and C. W. Chen, The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures, Mol Microbiol, vol.28, pp.905-916, 1998.

C. W. Chen, C. Huang, H. Lee, H. Tsai, and R. Kirby, Once the circle has been broken: dynamics and evolution of Streptomyces chromosomes, Trends Genet, vol.18, issue.02, p.2752, 2002.

A. Thibessard and P. Leblond, Subtelomere plasticity in the bacterium Streptomyces, Louis EJ, Becker MM, pp.243-258, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01478830

J. R. Doroghazi and D. H. Buckley, Widespread homologous recombination within and between Streptomyces species, ISME J, vol.4, pp.1136-1143, 2010.

H. Ochman, J. G. Lawrence, and E. A. Groisman, Lateral gene transfer and the nature of bacterial innovation, Nature, vol.405, pp.299-304, 2000.

C. Stuttard, Temperate phages of Streptomyces venezuelae: lysogeny and host specificity shown by phages SV1 and SV2, Microbiology, vol.128, pp.115-121, 1982.

J. Burke, D. Schneider, and J. Westpheling, Generalized transduction in Streptomyces coelicolor, Proc Natl Acad Sci, vol.98, pp.6289-6294, 2001.

E. Bordeleau, M. G. Ghinet, and V. Burrus, Diversity of integrating conjugative elements in actinobacteria: coexistence of two mechanistically different DNA-translocation systems, Mob Genet Elements, vol.2, pp.119-124, 2012.

L. Thoma and G. Muth, Conjugative DNA-transfer in Streptomyces, a mycelial organism, Plasmid, vol.87, pp.1-9, 2016.

G. S. Pettis, Spreading the news about the novel conjugation mechanism in Streptomyces bacteria, Environ Microbiol Rep, vol.10, pp.503-510, 2018.

B. R. Mcdonald and C. R. Currie, Lateral gene transfer dynamics in the ancient bacterial genus Streptomyces, vol.8, pp.644-661, 2017.

A. Stien, D. Eparvier, V. Parrot, D. Tomasi, S. Suzuki et al., Multiple Streptomyces species with distinct secondary metabolomes have identical 16S rRNA gene sequences, Sci Rep, vol.7, p.11089, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01590493

K. Vetsigian, R. Jajoo, and R. Kishony, Structure and evolution of Streptomyces interaction networks in soil and in silico, PLoS Biol, vol.9, 2011.

C. M. Vicente, A. Thibessard, J. Lorenzi, M. Benhadj, L. Hôtel et al., Comparative genomics among closely related Streptomyces strains revealed specialized metabolite biosynthetic gene cluster diversity, Antibiotics (Basel), vol.7, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01887213

H. Harris, M. Bourin, M. J. Claesson, and P. W. O'toole, Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal, Microb Genom, vol.3, 2017.

C. J. Park and C. P. Andam, Within-species genomic variation and variable patterns of recombination in the tetracycline producer Streptomyces rimosus, Front Microbiol, vol.10, p.552, 2019.

N. J. Croucher, P. G. Coupland, A. E. Stevenson, A. Callendrello, S. D. Bentley et al., Diversification of bacterial genome content through distinct mechanisms over different timescales, Nat Commun, vol.5, p.5471, 2014.

I. Levade, Y. Terrat, J. Leducq, A. A. Weil, L. M. Mayo-smith et al., Vibrio cholerae genomic diversity within and between patients, Microb Genom, vol.3, 2017.

H. Bruns, M. Crüsemann, A. Letzel, M. Alanjary, J. O. Mcinerney et al., Function-related replacement of bacterial siderophore pathways, ISME J, vol.12, pp.320-329, 2018.

P. Stefanic, B. Kraigher, N. A. Lyons, R. Kolter, and I. Mandic-mulec, Kin discrimination between sympatric Bacillus subtilis isolates, Proc Natl Acad Sci U S A, vol.112, pp.14042-14047, 2015.

S. Wielgoss, X. Didelot, R. R. Chaudhuri, X. Liu, G. D. Weedall et al., A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus, ISME J, vol.10, pp.2468-2477, 2016.

M. Vos, A. B. Wolf, S. J. Jennings, and G. A. Kowalchuk, Micro-scale determinants of bacterial diversity in soil, FEMS Microbiol Rev, vol.37, pp.936-954, 2013.

A. B. Wolf, M. Vos, W. De-boer, and G. A. Kowalchuk, Impact of matric potential and pore size distribution on growth dynamics of filamentous and non-filamentous soil bacteria, PLoS One, vol.8, p.83661, 2013.

X. Raynaud and N. Nunan, Spatial ecology of bacteria at the microscale in soil, PLoS One, vol.9, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01252483

E. W. Sayers, R. Agarwala, E. E. Bolton, J. R. Brister, K. Canese et al., Database resources of the National Center for Biotechnology Information, Nucleic Acids Res, vol.47, pp.23-28, 2019.

T. Wenner, V. Roth, G. Fischer, C. Fourrier, B. Aigle et al., End-to-end fusion of linear deleted chromosomes initiates a cycle of genome instability in Streptomyces ambofaciens, Mol Microbiol, vol.50, pp.411-425, 2003.
URL : https://hal.archives-ouvertes.fr/hal-01659028

G. Fischer, T. Wenner, B. Decaris, and P. Leblond, Chromosomal arm replacement generates a high level of intraspecific polymorphism in the terminal inverted repeats of the linear chromosomal DNA of Streptomyces ambofaciens, Proc Natl Acad Sci U S A, vol.95, pp.14296-14301, 1998.
URL : https://hal.archives-ouvertes.fr/hal-01625341

T. Uchida, M. Miyawaki, and H. Kinashi, Chromosomal arm replacement in Streptomyces griseus, J Bacteriol, vol.185, pp.1120-1124, 2003.

S. Clerc and P. Simonet, Efficiency of the transfer of a pSAM2-derivative plasmid between two strains of Streptomyces lividans in conditions ranging from agar slants to non-sterile soil microcosms, FEMS Microbiol Ecol, vol.21, pp.157-165, 1996.

J. T. Sullivan and C. W. Ronson, Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene, Proc Natl Acad Sci U S A, vol.95, pp.5145-5149, 1998.

K. Blin, T. Wolf, M. G. Chevrette, X. Lu, C. J. Schwalen et al., 0-improvements in chemistry prediction and gene cluster boundary identification, Nucleic Acids Res, vol.45, pp.36-41, 2017.

J. O. Mcinerney, A. Mcnally, and M. J. O'connell, Why prokaryotes have pangenomes, Nat Microbiol, vol.2, p.17040, 2017.

G. Hoff, C. Bertrand, E. Piotrowski, A. Thibessard, and P. Leblond, Genome plasticity is governed by double strand break DNA repair in Streptomyces, Sci Rep, vol.8, p.5272, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01757262

S. Casjens, N. Palmer, R. Van-vugt, W. M. Huang, B. Stevenson et al., A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi, Mol Microbiol, vol.35, pp.490-516, 2002.

M. Ricchetti, B. Dujon, and C. Fairhead, Distance from the chromosome end determines the efficiency of double strand break repair in subtelomeres of haploid yeast, J Mol Biol, vol.328, issue.03, pp.315-317, 2003.

E. V. Linardopoulou, E. M. Williams, Y. Fan, C. Friedman, J. M. Young et al., Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication, Nature, vol.437, pp.94-100, 2005.

S. D. Bentley, K. F. Chater, A. Cerdeño-tárraga, G. L. Challis, N. R. Thomson et al., , 2002.

, Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2), Nature, vol.417, pp.141-147

N. Hsiao and K. R. , Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system, Antonie Van Leeuwenhoek, vol.93, pp.1-25, 2008.

D. A. Hopwood, Soil to genomics: the Streptomyces chromosome, Annu Rev Genet, vol.40, pp.1-23, 2006.

D. A. Hopwood, T. Kieser, H. M. Wright, and M. J. Bibb, Plasmids, recombination and chromosome mapping in Streptomyces lividans 66, J Gen Microbiol, vol.129, pp.2257-2269, 1983.

T. A. Gray, J. A. Krywy, J. Harold, M. J. Palumbo, and K. M. Derbyshire, Distributive conjugal transfer in mycobacteria generates progeny with meioticlike genome-wide mosaicism, allowing mapping of a mating identity locus, PLoS Biol, vol.11, 2013.

K. M. Derbyshire and T. A. Gray, Distributive conjugal transfer: new insights into horizontal gene transfer and genetic exchange in mycobacteria, Microbiol Spectr, vol.2, pp.2-0022, 2014.

O. X. Cordero, H. Wildschutte, B. Kirkup, S. Proehl, L. Ngo et al., Ecological populations of bacteria act as socially cohesive units of antibiotic production and resistance, Science, vol.337, pp.1228-1231, 2012.

M. I. Abrudan, F. Smakman, A. J. Grimbergen, S. Westhoff, E. L. Miller et al., Socially mediated induction and suppression of antibiosis during bacterial coexistence, Proc Natl Acad Sci U S A, vol.112, pp.11054-11059, 2015.

E. Butait?, M. Baumgartner, S. Wyder, and R. Kümmerli, Siderophore cheating and cheating resistance shape competition for iron in soil and freshwater Pseudomonas communities, Nat Commun, vol.8, p.414, 2017.

V. M. D'costa, K. M. Mcgrann, D. W. Hughes, and G. D. Wright, Sampling the antibiotic resistome, Science, vol.311, pp.374-377, 2006.

T. Kieser, M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood, Practical Streptomyces genetics, John Innes Foundation, 2000.

T. Tatusova, M. Dicuccio, A. Badretdin, V. Chetvernin, E. P. Nawrocki et al., NCBI prokaryotic genome annotation pipeline, Nucleic Acids Res, vol.44, pp.6614-6624, 2016.

J. Sun, G. H. Kelemen, J. M. Fernández-abalos, and M. J. Bibb, Green fluorescent protein as a reporter for spatial and temporal gene expression in Streptomyces coelicolor A3(2), Microbiology, vol.145, pp.2221-2227, 1999.

M. Kim, H. Ha, and S. Choi, Conjugal transfer using the bacteriophage phiC31 att/int system and properties of the attB site in Streptomyces ambofaciens, Biotechnol Lett, vol.30, pp.695-699, 2008.

P. Leblond, F. X. Francou, J. Simonet, and B. Decaris, Pulsed-field gel electrophoresis analysis of the genome of Streptomyces ambofaciens strains, FEMS Microbiol Lett, vol.72, pp.79-88, 1990.
URL : https://hal.archives-ouvertes.fr/hal-01658692

H. Rintala, A. Nevalainen, E. Rönkä, and M. Suutari, PCR primers targeting the 16S rRNA gene for the specific detection of streptomycetes, Mol Cell Probes, vol.15, pp.337-347, 2001.

Y. Guo, W. Zheng, X. Rong, and Y. Huang, A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics, Int J Syst Evol Microbiol, vol.58, pp.149-159, 2008.

S. Kumar, G. Stecher, and K. Tamura, MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets, Mol Biol Evol, vol.33, pp.1870-1874, 2016.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J Mol Biol, vol.215, issue.05, pp.80360-80362, 1990.

R. C. Edgar, MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, vol.5, p.113, 2004.

G. Talavera and J. Castresana, Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments, Syst Biol, vol.56, pp.564-577, 2007.

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, pp.1312-1313, 2014.

J. Goris, K. T. Konstantinidis, J. A. Klappenbach, T. Coenye, P. Vandamme et al., DNA-DNA hybridization values and their relationship to whole-genome sequence similarities, Int J Syst Evol Microbiol, vol.57, pp.81-91, 2007.

A. M. Eren, Ö. C. Esen, C. Quince, J. H. Vineis, H. G. Morrison et al., Anvi'o: an advanced analysis and visualization platform for 'omics data, PeerJ, vol.3, 2015.

, mbio.asm.org, vol.10, pp.1533-1552, 2019.