dickeya sp  (ATCC)

Journal: bioRxiv

Article Title: Dickeya ananae sp. nov., pectinolytic bacterium isolated from pineapple ( Ananas comosus )

doi: 10.1101/2024.10.29.620964

Figure Lengend Snippet: Heatmap displaying combined ANI and dDDH values. ANI values (above diagonal) were calculated using the OrthoANI algorithm in OAT software; dDDH values (below diagonal) were determined using the Genome-to-Genome Distance Calculator (GGDC) version 3.0 ( https://ggdc.dsmz.de/ ). The analysis includes the type strains of each Dickeya species and D. ananae sp. nov. strain A5410 T .

Article Snippet: The 16S rRNA phylogenetic tree was later constructed by uploading the whole genome sequences of the seven strains used in this study, along with 37 whole genomes of other Dickeya species, to the Type Strain Genome Server (TYGS at https://tygs.dsmz.de ).

Techniques: Software

Journal: bioRxiv

Article Title: Dickeya ananae sp. nov., pectinolytic bacterium isolated from pineapple ( Ananas comosus )

doi: 10.1101/2024.10.29.620964

Figure Lengend Snippet: Whole genome sequence-based phylogenetic tree of the genus Dickeya . This tree wa constructed using the Type Strain Genome Server (TYGS), it shows the relationships between D. ananae sp. nov. A5410 T and strains of different Dickeya species. The tree was inferred with FastME 2.1.6.1 using the Genome BLAST Distance Phylogeny (GBDP) approach, with distances calculated from genome sequences via the TYGS server. Branch lengths are scaled in terms of GBDP distance formula d5. The numbers above the branches are GBDP pseudo-bootstrap support values >60% from 100 replications, with an average branch support of 92.7%. The tree was rooted at the midpoint (Farris, 1972). Leaf labels are annotated by affiliation to species and subspecies clusters, genomic G+C content, δ values and overall genome sequence length, number of proteins, and the kind of strain. The phylogenetic trees with bootstrapping value and colored annotations were created using web-based tool Interactive Tree of Life (iTOL v6).

Article Snippet: The 16S rRNA phylogenetic tree was later constructed by uploading the whole genome sequences of the seven strains used in this study, along with 37 whole genomes of other Dickeya species, to the Type Strain Genome Server (TYGS at https://tygs.dsmz.de ).

Techniques: Sequencing, Construct

Journal: International journal of systematic and evolutionary microbiology

Article Title: Dickeya lacustris sp. nov., a water-living pectinolytic bacterium isolated from lakes in France.

doi: 10.1099/ijsem.0.003208

Figure Lengend Snippet: Fig. 2. Phylogenetic position of D. lacustris based on gapA gene sequences. The evolutionary history was inferred using the neighbour- joining method [27]. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 rep- licates) are shown next to the branches [28]. Evolutionary distances (number of base substitutions per site, 1005 positions) were com- puted using the maximum composite likelihood method [29]. Evolutionary analyses were conducted in MEGA7 [30]. This analysis was performed using the gapA gene sequences of the Dickeya type strains, Pectobacterium type strains and five D. lacustris strains. Serratia fonticola was used as an outgroup. Bar, 0.01 changes per nucleotide position.

Article Snippet: The calculation of isDDH values, using the D. lacustris S29T genome as a reference and other Dickeya genomes as queries (http://ggdc.dsmz.de/) (Table S1), gave values lower than 33%.

Techniques:

Journal: bioRxiv

Article Title: The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

doi: 10.1101/568105

Figure Lengend Snippet: Maximal likelihood phylogeny (left) of 1,341 Dickeya single copy protein families (50 sequences, 414,696 amino acid positions). The tree was computed with IQ-TREE with the LG+C60 model and rooted using Serratia ATCC 39006. Numbers associated to branches correspond to ultrafast bootstrap values. The scale bar corresponds to evolutionary distance (i.e. the average number of the substitutions inferred per site). The table (right) corresponds to the S AB association coefficient computed for each pair of strains as S AB =(100×2 N AB )/( N A + N B ), in which N A is the number of protein families present in strain A, N B is the number of protein families present in strain B and N AB is the number of protein families shared by strain A and strain B. This coefficient ranged from 0 when both strains do not share any gene family to 100 when all the families present in strain A were also present in strain B. The figure was generated using Evolview .

Article Snippet: Yet, the large evolutionary distance between ATCC 39006 strain and Dickeya (Supplementary Figure S1), its lower GC content (49.2% vs 52.6 - 56.9% in Dickeya ) (Supplementary Table S3), and the lower number of protein families shared between ATCC 39006 and Dickeya (60.5%) compared to between Dickeya species (64.7% - 89.6%, Supplementary Table S5), suggested that strain ATCC 39006 does not belong to Dickeya and represents rather a close but distinct lineage, possibly a new genus, that we propose to call Prodigiosinella , with strain ATCC 39006 being reclassified as Prodigiosinella confusarubida .

Techniques: Generated