Summary Dickeya is a genus of phytopathogenic enterobacterales causing soft rot in a variety of plants (e.g. potato, chicory, maize). Among the species affiliated to this genus, Dickeya aquatica, described in 2014, remained particularly mysterious because it had no known host. Furthermore, while D. aquatica was proposed to represent a deep‐branching species among Dickeya genus, its precise phylogenetic position remained elusive. Here, we report the complete genome sequence of the D. aquatica type strain 174/2. We demonstrate the affinity of D. aquatica strain 174/2 for acidic fruits such as tomato and cucumber and show that exposure of this bacterium to acidic pH induces twitching motility. An in‐depth phylogenomic analysis of all available Dickeya proteomes pinpoints D. aquatica as the second deepest branching lineage within this genus and reclassifies two lineages that likely correspond to new genomospecies (gs.): Dickeya gs. poaceaephila (Dickeya sp NCPPB 569) and Dickeya gs. undicola (Dickeya sp 2B12), together with a new putative genus, tentatively named Prodigiosinella. Finally, from comparative analyses of Dickeya proteomes, we infer the complex evolutionary history of this genus, paving the way to study the adaptive patterns and processes of Dickeya to different environmental niches and hosts. In particular, we hypothesize that the lack of xylanases and xylose degradation pathways in D. aquatica could reflect adaptation to aquatic charophyte hosts which, in contrast to land plants, do not contain xyloglucans.

24 42 phylogenetic position remained elusive. 43 Here, we report the complete genome sequence of the D. aquatica type strain 174/2. We 44 demonstrate the affinity of D. aquatica T for acidic fruits such as tomato and cucumber, and show 45 that exposure of this bacterium to acidic pH induces twitching motility. An in-depth phylogenomic 46 analysis of all available Dickeya proteomes pinpoints D. aquatica as the second deepest branching 47 lineage within this genus and reclassifies two lineages that likely correspond to new 48 genomospecies (gs.): Dickeya gs. poaceaephila (Dickeya sp NCPPB 569) and Dickeya gs.49 undicola (Dickeya sp 2B12), together with a new putative genus, tentatively named Prodigiosinella.50Finally, from comparative analyses of Dickeya proteomes we infer the complex evolutionary history 51 of this genus, paving the way to study the adaptive patterns and processes of Dickeya to different 52 3 environmental niches and hosts. In particular, we hypothetize that the lack of xylanases and xylose 53 degradation pathways in D. aquatica could reflects adaptation to aquatic charophyte hosts which, 54 in contrast to land plants, do not contain xyloglucans. 55 56 Introduction 57 Enterobacterales represent one of the most studied orders of Gammaproteobacteria. According to 58 current systematics, Enterobacterales are divided into eight families: Enterobacteriaceae, 59 Yersiniaceae, Thorselliaceae, Hafniaceae, Morganellaceae, Budviciaceae, Erwiniaceae, and 60 Pectobacteriaceae. Enterobacterales are widespread, being found in very different environments 61 such as soils, fresh water, ocean, sediments, and many of them are associated with plants and 62 animals, including insects and humans (Brenner and Farmer III, 2005). Enterobacterales include 63 also important model organisms such as Escherichia coli, human pathogens such as Salmonella, 64 Shigella, and Yersinia (Dekker and Frank, 2015), and plant pathogens such as Erwiniaceae (e.g. 65 Erwinia, Pantoea, Phaseolibacter) and Pectobacteriaceae (e.g. Pectobacterium, Dickeya, 66 Brenneria, Lonsdalea) (Hauben et al., 1998; Samson et al., 2005). These phytopathogens share 67 virulence genes with zoopathogens such as type III secretion systems (T3SS) that inject effector 68 proteins in eukaryotic cells to suppress the host innate immune defence (Buttner, 2016). They also 69 produce specialized plant virulence factors such as pectinases found in pectinolytic bacteria 70 (Hugouvieux-Cotte-Pattat et al., 2014). 71Among pectinolytic enterobacterales, Dickeya is the causative agent of soft rot in a wide variety of 72 plants including economically important crops (e.g. potato, chicory, maize, rice, tomato, sugar beet, 73 pineapple, banana) and many ornamental plants (Ma et al., 2007). This causes substantial 74 production losses amounting, for instance for potato, to tens of millions of Euros/year in Europe 75 (Toth et al., 2011). The Dickeya genus was first described by Samson et al. (2005), who initially 76 distinguished six species: Dickeya dadantii, Dickeya dieffenbach...