- Comparative genomics and pangenome- oriented studies reveal high homogeneity of the agronomically relevant. - Attribution of the genes included in the D.. - Full list of author information is available at the end of the article. - solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.. - Because of the activities of PCWDEs, these necro- trophic bacteria get access to valuable sources of nutrients accumulated within the plant cell. - Such a molecular or adaptive repertoire takes part in progression of the incited infection. - Typical blackleg symptoms comprise water-soaked, blackened stem base in addition to chlorosis and wilting of the leaves [2]. - Assessment of the total economic impact of these diseases is demanding as Pecto- bacterium and Dickeya spp. - Importantly, such a number of sequences turned out to be sufficient to report in this work an almost closed status of the pangenome of D. - N 50 , which refers to the minimum length of contigs in which half of the bases of the assembly are covered, ranged from 755,734 bp to 4,934,537 bp (for IFB0695 or IFB0421. - For the origin and the annotated genomic features of the herein included Dickeya solani reference strains see our former study Golanowska et al. - of contigs that comprise half of the genome size, spanned from 1 to 2 (Table 2). - None of the contigs from de novo assembled D. - The number of protein-coding genes varied from 4143 (IFB0212) to 4446 (IFB0417), while the quantities of the annotated rRNA and tRNA amounted to 18–22 and 72–75, respectively (Table 1).. - solani sequences (versions of the genomes available in the Genbank database at a time of conducting research have been included. - 7) are also in favour of the genome assembly pipeline used for the newly sequenced genomes. - Regarding rRNA, solely 1 to 4 such genes were annotated for the included versions of the reference genomes of PPO 9019, RNS 05.1.2A, RNS 07.7.3B, IPO 2222, GBBC 2040, MK10, MK16, PPO 9134, IFB0158 and IFB0221 strains [31], in contrast to 18–22 detected in the herein re- ported de novo sequenced genomes (Table 1).. - The versions of the included reference genomes are the ones downloaded from the Genbank database for Golanowska et al. - Thus, we postulate that the number of the annotated rRNA-encoding genes might be regarded as an inform- ative marker of the achieved quality of de novo assembly of D. - 1), regardless of the sequencing method used or the closed/draft status of the genome assembly. - Undoubt- edly, the genome of RNS 05.1.2A stands out from the pool of the tested sequences, not only taking into consideration the number, but also the size of the missing regions. - In addition, 1.0 correlation of the tetra-nucleotide signatures was likewise not rarely exhibited by the studied se- quences (Supplementary Table 3). - solani genomes showed that genes) of the gene pool grouped into the core genes) to the accessory and genes) to the unique pangenome fraction. - In the current research, we significantly enlarged the number of the included D. - The obtained data showed that contribution of the core genome increased to genes) while the accessory and unique pangenome fractions shrank to either 7.2% (318 genes) or 8.1% (356 genes) of the whole D. - Thirteen of the D. - Each of the depicted rings refers to one D.. - Construction and extrapo- lation of the core- and pan-genome plots (Fig. - 2B), calculated with the use of the exponential curve fit model and power-law regression model, respectively, revealed that with the b parameter equalling the pangenome of D. - Functional assignment of the D. - solani pangenome fractions The outcomes of the attribution of the Clusters of Orthologous Groups (COGs) functional categories to the core, accessory and unique gene pools of 22 D.. - Abundancy of the core, accessory and unique pangenome fractions within the pangenome of D. - The largest number of the assigned unique COGs derived from the genome of RNS 05.1.2A (106) followed by IFB0487 (8), IFB0417 (4) IFB0421 (1) and MK10 (1) (Supplemen- tary Table 4). - Among the functional roles of the assigned unique D. - In the first large clade of the gener- ated neighbour-joining phylogenetic tree computed on concatenated core gene alignments (Fig. - Rather, no obvious correlation between the geographical origin of the strains and the computed genome-wide rela- tionships profiting from the core fraction was observed.. - Among achievements of this work, one should notice further proofs for high potency of the herein applied genome assembly pipeline described for the first time in our former work [31]. - Interestingly, the sequence of RNS 08.23.3.1A was later on improved by Khayi et al into a fully closed chromosome containing the N bases by applica- tion of scaffolding, home-made scripts in addition to Sanger sequencing of the PCR amplicons. - The resulting assembly contained 5,094,121 bp (%GC 56.40), exceeding by 161, 201 bp the improved closed circular genome of IFB0099 (%GC 56.24) obtained with the use of the developed genome assembly pipeline [31]. - In spite of the same annotation software utilized, the total number of protein-coding genes, i.e. - This laborious and costly approach yielded a genome consisting finally of 4 contigs, which discloses obvious benefits of the herein utilized genome assembly pipeline. - values reported for the first released versions of the above- mentioned genomes were much lower (from 40,901 to 485,700, for GBBC 2040 and MK16, respectively [44]) than in the case of the revised versions included here as references. - 4 Phylogenetic analysis of the studied Dickeya solani strains based on concatenated core gene alignments. - Flags mark the countries of origin of the included D. - Also schematic representation of the environmental source (potato tissue, hyacinth tissue, river water or potato rhizosphere) of each D. - number of the incorporated N bases is still quite large. - [44], IPO 2222 was reported to possess 4,857,348 bp, the version of this genome included in the here-presented research exhibits 4,867,258 bp, while the length of the one that might be currently downloaded from the Genbank database equals 4,919,833 bp. - One of the reasons behind undertaking search for plasmids in draft genomic sequences of D. - solani is that the occurrence of such extrachromosomal molecules might be an explanation for the contig-based status of the assembly. - solani D s0432–1 to several other members of the Dickeya genus, i.e. - solani RNS 05.1.2A clearly stood out from the other analysed both in terms of the genomic structure and the computed pairwise- comparisons is putatively associated with the abundance of unique genes as further proven in the pangenome-related section and suggested in the former studies [31, 39].. - [39] postulated HGT from a closely related habitant of the same ecological niche, namely D. - The fact that both PPO 9019 and PPO 9134 strains were acquired from hyacinths and stood out solely in the ANI calculations, in contrast to the computed correl- ation indexes of the tetra-nucleotide signatures, might be a point in favour of the HGT-based hypothesis.. - Importantly, with the applied number of whole genomic sequences, the almost closed status of the D. - solani, we reported that another member of the Pectobacteriaceae family, namely Pecto- bacterium parmentieri, possesses an open pangenome [93]. - We associated the overrepresentation of the dispensable pangenome part with high genomic plasti- city of P. - pangenome status of a species might have been affected by the number and representativeness of the genomes selected for the analysis [94]. - Attribution of the genes originating from diverse D.. - solani genomes, the majority of the strains harbored 2–3 pro- phages with the exception of RNS 05.1.2A, which showed the presence of 7 such prophage-like elements [31]. - Furthermore, quite a big number of the observed transcription- associated unique COGs confirms the assumptions of Potrykus et al. - solani strains showed no obvi- ous correlations between the geographical origin of the isolates and their evolutionary relationships. - solani strains is impaired to some degree by high similarity of these isolates and their tendency to group together regardless of the origin and year of isolation. - The assign- ment of the genes included in the D. - After proposal of the PacBio-based optimal genome assembly pipeline for D. - solani [31], DNA of the latter 4 D. - To assure the uniformity of the attributed genomic annotations, also the reference D. - The included pairwise genome comparisons are based on ANIb, ANIm and computation of the correlation indexes of the tetra- nucleotide signatures by applying JSpecies webserver (accessed . - Further computation of the output led to the generation of a tab delimited gene presence/absence binary matrix (pan-matrix), utilized for pangenome pattern calculations with iterations (20 as a default). - was implemented for functional assignments on the basis of the best hits with the reference COG database [109]. - Percentage occur- rences of the assigned COG categories were calculated by BPGA v. - The upper number refers to the ANIb value while the lower depicted in parentheses is the percentage of the aligned sequences.. - The upper number refers to ANIm value while the lower depicted in parentheses is the percentage of the aligned sequences.. - Correlation indexes of the tetra-nucleotide signatures computed for the studied Dickeya solani genomes. - Description of data: Computation of the correlation indexes of the tetra-nucleotide signatures was conducted with JSpecies [106].. - The functions of the unique Dickeya solani COGs. - Yeshitila Degefu for provision of the VIC-BL-25 (IFB0231) D.. - All authors read and approved the final version of the manuscript.. - The funding bodies played no role in the design of the study, analysis and interpretation of data and in writing the manuscript.. - Data generated in this whole genome sequencing project are available in the Genome database of the National Center for Biotechnology Information (NCBI) under the BioProject PRJNA611911. - The assembled and annotated full genomic sequences of the herein de novo sequenced D.. - The datasets generated and/or analyzed during this study will not be publicly available prior to first publication of the herein presented manuscript. - We obtained permissions for the isolation of the studied bacterial isolates from plant samples collected by the National Inspectorates of Plant Health and Seed Inspection Service in Poland. - All described field studies were conducted in accordance with the policies of the National Inspectorates of Plant Health and Seed Inspection Service in Poland.. - Genome-based phylogeny and taxonomy of the ‘ Enterobacteriales. - Ecology of the soft rot Erwinias. - nov., emendation of the. - description of the genus Brenneria, reclassification of Dickeya. - nov., and emendation of the description of Dickeya dadantii. - Report of the ad hoc committee on the reconciliation of approaches to bacterial systematics. - Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences. - Complete genome anatomy of the emerging potato pathogen Dickeya solani type strain IPO 2222T.. - Genome sequence of the emerging plant pathogen Dickeya solani strain RNS 08.23.3.. - Estimating the size of the bacterial pan-genome.. - Draft genome sequence of a highly virulent strain of the plant pathogen Dickeya solani, IFB0099. - Structural identification of the O-antigen fraction from the. - lipopolysaccharide of the Burkholderia ambifaria strain 19182. - nov., a novel member of the Burkholderia cepacia complex including biocontrol and cystic fibrosis-related isolates. - A re-evaluation of the taxonomy of. - Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium. - Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model
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