Phylogenomic analysis of the Erwiniaceae supports reclassification of Kalamiella piersonii to Pantoea piersonii comb. nov. and Erwinia gerundensis to the new genus Duffyella gen. nov. as Duffyella gerundensis comb. nov

Transfer of Erwinia toletana and Erwinia iniecta to a novel genus Winslowiella gen. nov. as Winslowiella toletana comb. nov. and Winslowiella iniecta comb. nov. and description of Winslowiella arboricola sp. nov., isolated from bleeding cankers on broadleaf hosts

“…“ E. beijingensis ” was situated on a separate branch on the border of this clade, further removed from the proposed novel genus but with 100% support. The phylogeny of the whole genome tree demonstrates the divergence within the genus Erwinia with three clear subgroups of species, as defined previously ( Soutar and Stavrinides, 2022 ) and confirms the proposal that E. iniecta and E. toletana should be reclassified within a novel genus along with the novel species.…”

“…The proposed novel species was confirmed as a new taxon in the concatenated MLSA phylogenetic tree ( Figure 1 ), as all strains formed a single cluster without any reference strains of Erwinia species with validly published names, with 100% bootstrap support. This cluster was in a well-supported clade (88%) with E. toletana and E. iniecta , corresponding to Subgroup 3 from Soutar and Stavrinides (2022) providing support for their transfer to a novel genus. “ Erwinia beijingensis ” was situated on a separate branch on the border of this clade, but without bootstrap support, suggesting that its position could change with the addition of further novel species.…”

“…Genus delineation criteria, based on AAI, have been suggested with species exhibiting > 76% AAI to the type strain of the type species of the genus, and all type strains within the genus sharing > 74% AAI to each other ( Nicholson et al, 2020 ). These cut-off values appear too relaxed for the Erwiniaceae , and Soutar and Stavrinides (2022) suggested that 79% may be an appropriate threshold for delineating genera within this family. However, several Erwinia species exhibited AAI values which can be considered “borderline.” The POCP values ( Supplementary Table 3 ) demonstrated a similar pattern with higher values (75–87%) observed between species of the proposed novel genus, and lower values (64–73%) to “ E. beijingensis ” and Erwinia species.…”

“…Partial 16S rRNA gene sequencing of the strains demonstrated ∼99% similarity to E. toletana , but phylogenetically they appeared to belong to a novel taxon. A recent study examining the phylogenomic relationships between species of the family Erwiniaceae , identified three subgroups of species in the genus Erwinia ( Soutar and Stavrinides, 2022 ). Subgroup 3 contained E. toletana and Erwinia iniecta and it was suggested that these species should be assigned to a novel genus.…”

Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734

“…The annotation of P. agglomerans DAPP-PG 734 plasmid 4, with its size of 117′499 bp the smallest plasmid in this strain, revealed that it contains a gene cluster encoding for an incomplete integrative conjugative element (Fig. 5), that shares a high similarity to ICE-based plasmid backbone regions of E. amylovora ACW56400 pEI70 [52], Erwinia billingiae Eb661 pE102 [53] and Duffyella gerundensis EM595 T pEM02 [54,55]. This ICE region lacks several tra and pil genes and conserved genes that are common to chromosomally integrated ICEs.…”