M. Adeolu, S. Alnajar, S. Naushad, and R. S. Gupta, Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for enterobacterales Ord. Nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. Nov., Pectobacteriaceae fam. Nov., Yersiniaceae fam. Nov., Hafniaceae fam. Nov., Morgane, Int J Syst Evol Microbiol, vol.66, pp.5575-99, 2016.

A. Charkowski, C. Blanco, G. Condemine, D. Expert, T. Franza et al., The role of secretion systems and small molecules in soft-rot Enterobacteriaceae pathogenicity, Annu Rev Phytopathol, vol.50, pp.425-474, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01190826

T. Joko, A. Subandi, N. Kusumandari, A. Wibowo, and A. Priyatmojo, Activities of plant cell wall-degrading enzymes by bacterial soft rot of orchid, Arch Phytopathol Plant Prot, vol.47, pp.1239-50, 2014.

S. Reverchon and W. Nasser, Dickeya ecology, environment sensing and regulation of virulence programme, Environ Microbiol Rep, vol.5, pp.622-658, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01997073

B. Ma, M. E. Hibbing, H. Kim, R. M. Reedy, I. Yedidia et al., Host range and molecular phylogenies of the soft rot enterobacterial genera Pectobacterium and Dickeya, Phytopathology, vol.97, pp.1150-63, 2007.

R. Samson, J. B. Legendre, R. Christen, . Fischer-le, M. Saux et al., Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. Nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Int J Syst Evol Microbiol, vol.55, pp.1415-1442, 2005.

J. M. Van-der-wolf, E. H. Nijhuis, M. J. Kowalewska, G. S. Saddler, N. Parkinson et al., Dickeya solani sp. nov., a pectinolytic plant-pathogenic bacterium isolated from potato (Solanum tuberosum), Int J Syst Evol Microbiol, vol.64, pp.768-74, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01208723

N. Parkinson, P. Devos, M. Pirhonen, and J. Elphinstone, Dickeya aquatica sp. nov., isolated from waterways, Int J Syst Evol Microbiol, vol.64, pp.2264-2270, 2014.
DOI : 10.1099/ijs.0.058693-0

URL : http://ijs.microbiologyresearch.org/deliver/fulltext/ijsem/64/7/2264_ijs058693.pdf?itemId=/content/journal/ijsem/10.1099/ijs.0.058693-0&mimeType=pdf&isFastTrackArticle=

Y. Tian, Y. Zhao, X. Yuan, J. Yi, J. Fan et al., Dickeya fangzhongdai sp. nov., a plant pathogenic bacterium isolated from pear trees (Pyrus pyrifolia), Int J Syst Evol Microbiol, vol.66, pp.2831-2836, 2016.

R. Suharjo, H. Sawada, and Y. Takikawa, Phylogenetic study of Japanese Dickeya spp. and development of new rapid identification methods using PCR-RFLP, J Gen Plant Pathol, vol.80, pp.237-54, 2014.

N. T. Ali?, M. Tu?ek-?nidari?, M. Peterka, M. Ravnikar, and T. Dreo, Putative new species of the genus Dickeya as major soft rot pathogens in Phalaenopsis orchid production, Plant Pathol, vol.66, pp.1357-68, 2017.

I. Onwueme, Taro cultivation in Asia and the Pacific, Rap Publication, vol.16, pp.1-9, 1999.

G. Mendoza, C. H. , B. Cubillos, E. F. , M. Varón et al., Cerón lasso M del S. agronomic evaluation of bunching onion in the Colombian cundiboyacense high plateau, Int. J Agron, vol.2018, pp.1-8, 2018.

?. Ali?, F. Van-gijsegem, J. Pédron, M. Ravnikar, and T. Dreo, Diversity within the novel Dickeya fangzhongdai sp., isolated from infected orchids, water and pears, Plant Pathol, vol.67, pp.1612-1632, 2018.

N. Parkinson, D. Stead, J. Bew, J. Heeney, L. Tsror et al., Dickeya species relatedness and clade structure determined by comparison of recA sequences, Int J Syst Evol Microbiol, vol.59, pp.2388-93, 2009.

?. Ali?, T. Nagli?, P. Llop, N. Toplak, S. Koren et al., Draft genome gequences of Dickeya sp. isolates B16 (NIB Z 2098) and S1 (NIB Z 2099) causing coft rot of Phalaenopsis orchids, Genome Announc, vol.3, pp.973-988, 2015.

R. K. Aziz, D. Bartels, A. A. Best, M. Dejongh, T. Disz et al., The RAST server: rapid annotations using subsystems technology, BMC Genomics, vol.9, p.75, 2008.
DOI : 10.1186/1471-2164-9-75

URL : https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-9-75

A. L. Delcher, K. A. Bratke, E. C. Powers, and S. L. Salzberg, Identifying bacterial genes and endosymbiont DNA with glimmer, Bioinformatics, vol.23, pp.673-682, 2007.
DOI : 10.1093/bioinformatics/btm009

URL : https://academic.oup.com/bioinformatics/article-pdf/23/6/673/11206341/btm009.pdf

J. P. Meier-kolthoff, A. F. Auch, H. Klenk, and M. Göker, Genome sequence-based species delimitation with confidence intervals and improved distance functions, BMC Bioinformatics, vol.14, p.60, 2013.
DOI : 10.1186/1471-2105-14-60

URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-60

G. Méric, K. Yahara, L. Mageiros, B. Pascoe, M. Maiden et al., A reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic Campylobacter, PLoS One, vol.9, p.92798, 2014.

P. Stothard, J. R. Grant, and G. Van-domselaar, Visualizing and comparing circular genomes using the CGView family of tools

V. Miele, S. Penel, and L. Duret, Ultra-fast sequence clustering from similarity networks with SiLiX, BMC Bioinformatics, vol.12, p.116, 2011.
DOI : 10.1186/1471-2105-12-116

URL : https://hal.archives-ouvertes.fr/hal-00698365

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1799, 2004.
DOI : 10.1093/nar/gkh340

URL : http://europepmc.org/articles/pmc390337?pdf=render

J. Castresana, Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis, Mol Biol Evol, vol.17, pp.540-52, 2000.

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst Biol, vol.59, pp.307-328, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

I. Letunic and P. Bork, Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Res, vol.44, pp.242-247, 2016.

D. Arndt, J. R. Grant, A. Marcu, T. Sajed, A. Pon et al., PHASTER: a better, faster version of the PHAST phage search tool, Nucleic Acids Res, vol.44, pp.16-21, 2016.

I. Grissa, G. Vergnaud, and C. Pourcel, CRISPRFinder: a web tool to identify clustered regularly interspace short palindromic repeats, Nucleic Acids Res, vol.35, pp.52-59, 2007.
DOI : 10.1093/nar/gkm360

URL : https://academic.oup.com/nar/article-pdf/35/suppl_2/W52/9585369/gkm360.pdf

P. Siguier, J. Perochon, L. Lestrade, J. Mahillon, and M. Chandler, ISfinder: the reference Centre for bacterial insertion sequences, Nucleic Acids Res, vol.34, pp.32-38, 2006.
DOI : 10.1093/nar/gkj014

URL : https://hal.archives-ouvertes.fr/hal-00021179

C. Bertelli, M. R. Laird, K. P. Williams, B. Y. Lau, G. Hoad et al., IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets, Nucleic Acids Res, vol.45, pp.30-35, 2017.
DOI : 10.1093/nar/gkx343

URL : https://academic.oup.com/nar/article-pdf/45/W1/W30/18137382/gkx343.pdf

J. D. Glasner, P. Liss, G. Plunkett, . Iii, A. Darling et al., ASAP, a systematic annotation package for community analysis of genomes, Nucleic Acids Res, vol.31, pp.147-51, 2003.

K. Blin, T. Wolf, M. G. Chevrette, X. Lu, C. J. Schwalen et al., AntiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification, Nucleic Acids Res, vol.45, pp.36-41, 2017.

J. Huerta-cepas, D. Szklarczyk, K. Forslund, H. Cook, D. Heller et al., EggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences, Nucleic Acids Res, vol.44, pp.286-93, 2016.

S. 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 Res, vol.25, pp.3389-402, 1997.

Y. Zhao, Y. Tian, L. X. Hu, and B. , complete genome sequence of a Dickeya fangzhongdai type strain causing bleeding canker of pear tree trunks

, Genome Announc, vol.6, pp.177-195, 2018.

K. Wallden, A. Rivera-calzada, and G. Waksman, Type IV secretion systems: versatility and diversity in function, Cell Microbiol, vol.12, pp.1203-1215, 2010.

J. Pédron, S. Mondy, R. Des-essarts, Y. Van-gijsegem, F. Faure et al., Genomic and metabolic comparison with Dickeya dadantii 3937 reveals the emerging Dickeya solani potato pathogen to display distinctive metabolic activities and T5SS/T6SS-related toxin repertoire, BMC Genomics, vol.15, pp.1-13, 2014.

C. E. Alvarez-martinez and P. J. Christie, Biological diversity of prokaryotic type IV secretion systems, Microbiol Mol Biol Rev, vol.73, pp.775-808, 2009.

S. K. Aoki, E. J. Diner, D. Roodenbeke, C. Burgess, B. R. Poole et al., A widespread family of polymorphic contact-dependent toxin delivery systems in bacteria, Nature, vol.468, pp.439-481, 2010.

S. Koskiniemi, J. G. Lamoureux, K. C. Nikolakakis, C. T'kint-de-roodenbeke, M. D. Kaplan et al., Rhs proteins from diverse bacteria mediate intercellular competition, Proc Natl Acad Sci U S A, vol.110, pp.7032-7039, 2013.

W. Nasser, C. Dorel, J. Wawrzyniak, F. Van-gijsegem, M. Groleau et al., Vfm a new quorum sensing system controls the virulence of Dickeya dadantii, Environ Microbiol, vol.15, pp.865-80, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01001772

K. Sivonen, N. Leikoski, D. P. Fewer, and J. Jokela, Cyanobactins-ribosomal cyclic peptides produced by cyanobacteria, Appl Microbiol Biotechnol, vol.86, pp.1213-1238, 2010.

M. C. Bagley, J. W. Dale, E. A. Merritt, and X. Xiong, Thiopeptide antibiotics, Chem Rev, vol.105, pp.685-714, 2005.

T. N. Petersen, S. Brunak, G. Von-heijne, and H. Nielsen, SignalP 4.0: discriminating signal peptides from transmembrane regions, Nat Methods, vol.8, pp.785-791, 2011.

L. Kall, A. Krogh, and E. Sonnhammer, Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server, Nucleic Acids Res, vol.35, pp.429-461, 2007.

A. P. Tomaras, C. W. Dorsey, R. E. Edelmann, and L. A. Actis, Attachment to and biofilm formation on abiotic surfaces by Acinetobacter baumannii: involvement of a novel chaperone-usher pili assembly system, Microbiology, vol.149, pp.3473-84, 2003.

A. , BMC Genomics, vol.20, p.34, 2019.

P. Horvath and R. Barrangou, CRISPR/Cas, the immune system of bacteria and archaea, Source Sci New Ser, vol.327, pp.167-70, 2010.

D. V. Mavrodi, J. E. Loper, I. T. Paulsen, and L. S. Thomashow, Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf5, BMC Microbiol, vol.9, p.8, 2009.

E. Grohmann, G. Muth, and M. Espinosa, Conjugative plasmid transfer in grampositive bacteria, Microbiol Mol Biol Rev, vol.67, pp.277-301, 2003.

G. W. Sundin and C. L. Bender, Dissemination of the strA-strB streptomycinresistance genes among commensal and pathogenic bacteria from humans, animals, and plants, Mol Ecol, vol.5, pp.133-176, 1996.

S. Khayi, P. Blin, J. Pédron, T. M. Chong, K. G. Chan et al., Population genomics reveals additive and replacing horizontal gene transfers in the emerging pathogen Dickeya solani, BMC Genomics, vol.16, pp.1-13, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01217226

L. Pritchard, S. Humphris, G. S. Saddler, N. M. Parkinson, V. Bertrand et al., Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences, Plant Pathol, vol.62, pp.587-96, 2013.

O. Lukjancenko, T. M. Wassenaar, and D. W. Ussery, Comparison of 61 sequenced Escherichia coli genomes, Microb Ecol, vol.60, pp.708-728, 2010.

N. Hugouvieux-cotte-pattat, G. Condemine, and V. E. Shevchik, Bacterial pectate lyases, structural and functional diversity, Environ Microbiol Rep, vol.6, pp.427-467, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02001305

J. Zhou, H. Zhang, J. Wu, Q. Liu, P. Xi et al., A novel multidomain polyketide synthase is essential for zeamine production and the virulence of Dickeya zeae, Mol Plant-Microbe Interact, vol.24, pp.1156-64, 2011.

J. Hellberg, M. A. Matilla, and G. Salmond, The broad-spectrum antibiotic, zeamine, kills the nematode worm Caenorhabditis elegans, Front Microbiol, vol.6, pp.1-13, 2015.

T. A. Schöner, S. Gassel, A. Osawa, N. J. Tobias, Y. Okuno et al., Aryl polyenes, a highly abundant class of bacterial natural products, are functionally related to antioxidative carotenoids, Chembiochem, vol.17, pp.247-53, 2016.

J. Li, F. Sugawara, J. Harper, H. Koshino, W. M. Hess et al., Oocydin a, a chlorinated macrocyclic lactone with potent anti-oomycete activity from Serratia marcescens, Microbiology, vol.145, pp.3557-64, 1999.

C. Thaning, C. J. Welch, J. J. Borowicz, R. Hedman, and B. Gerhardson, Suppression of Sclerotinia sclerotiorum apothecial formation by the soil bacterium Serratia plymuthica: identification of a chlorinated macrolide as one of the causal agents, Soil Biol Biochem, vol.33, pp.1817-1843, 2001.

M. A. Matilla, H. Stöckmann, F. J. Leeper, and G. Salmond, Bacterial biosynthetic gene clusters encoding the anti-cancer haterumalide class of molecules: biogenesis of the broad spectrum antifungal and anti-oomycete compound, oocydin a, J Biol Chem, vol.287, pp.39125-39163, 2012.

I. Holtsmark, V. Eijsink, and M. B. Brurberg, Bacteriocins from plant pathogenic bacteria, FEMS Microbiol Lett, vol.280, pp.1-7, 2008.

R. Grinter, J. Milner, and D. Walker, Bacteriocins active against plant pathogenic bacteria, Biochem Soc Trans, vol.40, pp.1498-502, 2012.

Y. Minowa, M. Araki, and M. Kanehisa, Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes, J Mol Biol, vol.368, pp.1500-1517, 2007.

M. Potrykus, M. Golanowska, N. Hugouvieux-cotte-pattat, and E. Lojkowska, Regulators involved in Dickeya solani virulence, genetic conservation, and functional variability, Mol Plant-Microbe Interact, vol.27, pp.700-711, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02001323