Y. Colin, O. Nicolitch, M. Turpault, and S. Uroz, Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities, Appl. Environ. Microbiol, vol.83, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01548673

A. S. Adams, Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio, ISME J, vol.5, pp.1323-1331, 2011.

R. H. Baltz, Natural product drug discovery in the genomic era: realities, conjectures, misconceptions, and opportunities, J. Ind. Microbiol. Biotechnol, vol.46, pp.281-299, 2019.

G. R. Lewin, Evolution and Ecology of Actinobacteria and Their Bioenergy Applications, Annu. Rev. Microbiol, vol.70, pp.235-254, 2016.

S. Casjens and W. M. Huang, Linear chromosomal physical and genetic map of Borrelia burgdorferi, the Lyme disease agent, Mol. Microbiol, vol.8, pp.967-980, 1993.

D. W. Wood, The genome of the natural genetic engineer Agrobacterium tumefaciens C58, Science, vol.294, pp.2317-2323, 2001.

M. P. Mcleod, The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse, Proc. Natl. Acad. Sci. USA, vol.103, pp.15582-15587, 2006.

H. Ikeda, Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis, Nat. Biotechnol, vol.21, pp.526-531, 2003.

D. Weaver, Genome plasticity in Streptomyces: identification of 1 Mb TIRs in the S. coelicolor A3(2) chromosome, Mol. Microbiol, vol.51, pp.1535-1550, 2004.

T. Wenner, 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

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

W. Chen, Chromosomal instability in Streptomyces avermitilis: major deletion in the central region and stable circularized chromosome, BMC Microbiol, vol.10, p.198, 2010.

F. Choulet, Intraspecific variability of the terminal inverted repeats of the linear chromosome of Streptomyces ambofaciens, J. Bacteriol, vol.188, pp.6599-6610, 2006.
URL : https://hal.archives-ouvertes.fr/hal-01659064

P. C. Chang and S. N. Cohen, Bidirectional replication from an internal origin in a linear streptomyces plasmid, Science, vol.265, pp.952-954, 1994.

C. Yang, S. Tseng, H. Pan, C. Huang, and C. W. Chen, Telomere associated primase Tap repairs truncated telomeres of Streptomyces, Nucleic Acids Res, vol.45, pp.5838-5849, 2017.

, Scientific RepoRtS |, vol.10, p.7720, 2020.

Y. Ohnishi, Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350, J. Bacteriol, vol.190, pp.4050-4060, 2008.

K. Goshi, Cloning and analysis of the telomere and terminal inverted repeat of the linear chromosome of Streptomyces griseus, J. Bacteriol, vol.184, pp.3411-3415, 2002.

R. Kirby and C. W. Chen, Genome architecture. In Streptomyces: Molcular Biology and Biotechnology, pp.5-26

Z. Qin and S. N. Cohen, Replication at the telomeres of the Streptomyces linear plasmid pSLA2, Mol. Microbiol, vol.28, pp.893-903, 1998.

S. H. Chou, L. Zhu, and B. R. Reid, Sheared purine x purine pairing in biology, J. Mol. Biol, vol.267, pp.1055-1067, 1997.

C. Huang, The telomere system of the Streptomyces linear plasmid SCP1 represents a novel class, Mol. Microbiol, vol.63, pp.1710-1718, 2007.

H. Tsai, C. Huang, A. M. Lin, and C. W. Chen, Terminal proteins of Streptomyces chromosome can target DNA into eukaryotic nuclei, Nucleic Acids Res, vol.36, p.62, 2008.

A. Tidjani, Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics. mBio, vol.10, 2019.

A. Tidjani, Genome Sequences of 11 Conspecific Streptomyces sp, Strains. Microbiol. Resour. Announc, vol.8, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02292599

R. K. Aziz, The RAST Server: rapid annotations using subsystems technology, BMC Genomics, vol.9, p.75, 2008.

M. Zuker, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Res, vol.31, pp.3406-3415, 2003.

S. Kosugi, M. Hasebe, M. Tomita, and H. Yanagawa, Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs, Proc. Natl. Acad. Sci. USA, vol.106, pp.10171-10176, 2009.

I. B. Dodd and J. B. Egan, Improved detection of helix-turn-helix DNA-binding motifs in protein sequences, Nucleic Acids Res, vol.18, pp.5019-5026, 1990.

A. Marchler-bauer, CDD/SPARCLE: functional classification of proteins via subfamily domain architectures, Nucleic Acids Res, vol.45, pp.200-203, 2017.

J. D. Thompson, D. G. Higgins, and T. J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res, vol.22, pp.4673-4680, 1994.

S. Kumar, G. Stecher, M. Li, C. Knyaz, K. Tamura et al., Molecular Evolutionary Genetics Analysis across Computing Platforms, Mol. Biol. Evol, vol.35, pp.1547-1549, 2018.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J. Mol. Biol, vol.215, pp.403-410, 1990.

A. C. Darling, B. Mau, F. R. Blattner, and N. T. Perna, Mauve: multiple alignment of conserved genomic sequence with rearrangements, Genome Res, vol.14, pp.1394-1403, 2004.

D. P. Martin, B. Murrell, A. Khoosal, and B. Muhire, Detecting and Analyzing Genetic Recombination Using RDP4, Methods Mol. Biol. Clifton NJ, vol.1525, pp.433-460, 2017.

P. González-torres, F. Rodríguez-mateos, J. Antón, and T. Gabaldón, Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes, mBio, vol.10, 2019.

O. Skovgaard, M. Bak, A. Løbner-olesen, and N. Tommerup, Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing, Genome Res, vol.21, pp.1388-1393, 2011.

G. Hoff, Multiple and Variable NHEJ-Like Genes Are Involved in Resistance to DNA Damage in Streptomyces ambofaciens, Front. Microbiol, vol.7, p.1901, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01521993

X. Pang, Functional angucycline-like antibiotic gene cluster in the terminal inverted repeats of the Streptomyces ambofaciens linear chromosome, Antimicrob. Agents Chemother, vol.48, pp.575-588, 2004.
URL : https://hal.archives-ouvertes.fr/hal-01659031

H. Kinashi, M. Shimaji-murayama, and T. Hanafusa, Integration of SCP1, a giant linear plasmid, into the Streptomyces coelicolor chromosome, Gene, vol.115, pp.35-41, 1992.

K. Cheng, X. Rong, and Y. Huang, Widespread interspecies homologous recombination reveals reticulate evolution within the genus Streptomyces, Mol. Phylogenet. Evol, vol.102, pp.246-254, 2016.

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

M. Yamasaki and H. Kinashi, Two chimeric chromosomes of Streptomyces coelicolor A3(2) generated by single crossover of the wildtype chromosome and linear plasmid scp1, J. Bacteriol, vol.186, pp.6553-6559, 2004.

V. Barbe, Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites, J. Bacteriol, vol.193, pp.5055-5056, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00628567

W. M. Huang, M. Robertson, J. Aron, and S. Casjens, Telomere exchange between linear replicons of Borrelia burgdorferi, J. Bacteriol, vol.186, pp.4134-4141, 2004.

G. Chaconas and K. Kobryn, Structure, function, and evolution of linear replicons in Borrelia, Annu. Rev. Microbiol, vol.64, pp.185-202, 2010.

B. Li, DNA double-strand breaks and telomeres play important roles in trypanosoma brucei antigenic variation, Eukaryot. Cell, vol.14, pp.196-205, 2015.

K. Bao and S. N. Cohen, Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces, Genes Dev, vol.15, pp.1518-1527, 2001.

C. Yang, The terminal proteins of linear Streptomyces chromosomes and plasmids: a novel class of replication priming proteins, Mol. Microbiol, vol.43, pp.297-305, 2002.

H. Suzuki, K. Marushima, Y. Ohnishi, and S. Horinouchi, A novel pair of terminal protein and telomere-associated protein for replication of the linear chromosome of Streptomyces griseus IFO13350, Biosci. Biotechnol. Biochem, vol.72, pp.2973-2980, 2008.