Comparative Genomics Highlights Reclassification of 3 Subspecies of <i>Pectobacterium carotovorum</i> as Distinct Species, Identification of 14 Newly Pathogenic Isolates, and Roles of Gene Horizontal Transfer in Enhancing <i>Pectobacterium</i> ’s Vir

Strains from the genus of <i>Pectobacterium</i> can cause soft rot in numerous important plants, leading to significant losses. 16S rRNA gene sequences reliably identify genera, but species identification is sometimes challenging due to indistinguishable species or strains and unrecognized new taxa. Therefore, a dependable and straightforward classification method is needed. In this study, we analyzed the complete genome sequence and predicted genome components of <i>Pectobacterium</i> strains. We also assessed their genetic relationships using average nucleotide identity and in silico DNA-DNA hybridization, alongside phylogenetic analysis. This was done by examining the whole-genome sequences of 14 new strains isolated in our laboratory, responsible for plant soft rot, and comparing them with 64 strains' genome sequences available in GenBank. The results reveal that three subspecies of <i>P. carotovorum</i> with genome sequences deposited in GenBank (PccS1, PCC21, and strain 67) need to be reclassified as separate species and also confirm that our new isolated strains are accurately categorized at the species level. Additionally, the virulence and adaptability of certain strains of <i>Pectobacterium</i> (PccS1, SCRI1043, and SCC3193) are influenced by horizontal acquisition genes. Furthermore, our findings suggest that the diversity in the <i>car</i> gene cluster among <i>Pectobacterium</i> strains likely stems from gene losing, as well as the auto-induced regulatory mechanisms underlying virulence determinant gene activation, and Car biosynthesis might act in different ways in PccS1, enhancing our knowledge of their genomic traits through comparative studies.