S. F. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: A new generation of protein database search programs, Nucleic Acids Research, vol.25, pp.3389-3402, 1997.

P. P. Chan and T. M. Lowe, GtRNAdb 2.0: An expanded database of transfer RNA genes identified in complete and draft genomes, Nucleic Acids Research, vol.44, pp.184-189, 2016.

K. Grammann, A. Volke, and H. J. Kunte, New type of osmoregulated solute transporter identified in halophilic members of the bacteria domain: TRAP transporter TeaABC mediates uptake of ectoine and hydroxyectoine in Halomonas elongata DSM 2581 T, Journal of Bacteriology, vol.184, pp.3078-3085, 2002.

M. Kanehisa, M. Furumichi, M. Tanabe, Y. Sato, and K. Morishima, KEGG: New perspectives on genomes, pathways, diseases and drugs, Nucleic Acids Research, vol.45, pp.353-361, 2017.

V. Kindzierski, S. Raschke, N. Knabe, F. Siedler, B. Scheffer et al., Osmoregulation in the halophilic bacterium Halomonas elongata: A case study for integrative systems biology, PLoS ONE, vol.12, 2017.

D. Koboldt, K. Chen, T. Wylie, D. Larson, M. Mclellan et al., VarScan: Variant detection in massively parallel sequencing of individual and pooled samples, Bioinformatics, vol.25, pp.2283-2285, 2009.

S. I. Kuhlmann, A. C. Terwisscha-van-scheltinga, R. Bienert, H. J. Kunte, and C. Ziegler, 1.55 Å structure of the ectoine binding protein TeaA of the osmoregulated TRAP-Transporter TeaABC from Halomonas elongata, Biochemistry, vol.47, pp.9475-9485, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01703644

B. Langmead and S. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, pp.357-359, 2012.

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The sequence alignment/map format and SAMtools, Bioinformatics, vol.25, pp.2078-2094, 2009.

Y. H. Lin, B. C. Chang, P. W. Chiang, and S. L. Tang, Questionable 16S ribosomal RNA gene annotations are frequent in completed microbial genomes, Gene, vol.416, pp.44-47, 2008.

C. D. Lu, Y. Itoh, Y. Nakada, and Y. Jiang, Functional analysis and regulation of the divergent spuABCDEFGH-spuI operons for polyamine uptake and utilization in Pseudomonas aeruginosa PAO1, Journal of Bacteriology, vol.184, pp.3765-3773, 2002.

E. P. Nawrocki, S. W. Burge, A. Bateman, J. Daub, R. Y. Eberhardt et al., Rfam 12.0: Updates to the RNA families database, Nucleic Acids Research, vol.43, pp.130-137, 2015.

P. Peters, E. A. Galinski, and H. G. Trüper, The biosynthesis of ectoine, FEMS Microbiology Letters, vol.71, pp.157-162, 1990.

F. Pfeiffer, A. Broicher, T. Gillich, K. Klee, J. Mejia et al., Genome information management and integrated data analysis with HaloLex, Archives of Microbiology, vol.190, pp.281-299, 2008.

F. Pfeiffer and D. Oesterhelt, A manual curation strategy to improve genome annotation: Application to a set of haloarchael genomes, Life (Basel), vol.5, pp.1427-1444, 2015.

K. Schwibbert, A. Marin-sanguino, I. Bagyan, G. Heidrich, G. Lentzen et al., A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581 T, Environmental Microbiology, vol.13, pp.1973-1994, 2011.

J. Shine and L. Dalgarno, The 3?-terminal sequence of Escherichia coli 16S ribosomal RNA: Complementarity to nonsense triplets and ribosome binding sites, Proceedings of the National Academy of Sciences, vol.71, pp.1342-1346, 1974.

C. Trapnell, L. Pachter, and S. Salzberg, Tophat: Discovering splice junctions with RNA-Seq, Bioinformatics, vol.25, pp.1105-1111, 2009.

U. Consortium, UniProt: The universal protein knowledgebase, Nucleic Acids Research, vol.42, pp.191-198, 2016.

A. Ventosa, J. J. Nieto, and A. Oren, Biology of moderately halophilic aerobic bacteria, Microbiology and Molecular Biology Reviews, vol.62, pp.504-544, 1998.

R. H. Vreeland, C. D. Litchfield, E. L. Martin, and E. Elliot, Halomonas elongata, a new genus and species of extremely salt-tolerant bacteria, International Journal of Systematic Bacteriology, vol.30, pp.485-495, 1980.

D. Wu, S. C. Lim, Y. Dong, J. Wu, F. Tao et al., Structural basis of substrate binding specificity revealed by the crystal structures of polyamine receptors SpuD and SpuE from Pseudomonas aeruginosa, Journal of Molecular Biology, vol.416, pp.697-712, 2012.

F. Pfeiffer, I. Bagyan, and G. Alfaro-espinoza, Revision and reannotation of the Halomonas elongata DSM 2581 T genome, MicrobiologyOpen, vol.6, p.465, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02000495

,