Analysis of the Taxonomy and Pathogenic Factors of Pectobacterium aroidearum L6 Using Whole-Genome Sequencing and Comparative Genomics

Abstract

Soft rot pectobacteria are devastating plant pathogens with a global distribution and a broad host range. Pectobacterium aroidearum L6, previously isolated from leaves of Syngonium podophyllum, is a pectolytic bacterial pathogen that causes typical soft rot on S. podophyllum. There is a shortage for genome data of P. aroidearum, which seriously hinders research on classification and pathogenesis of Pectobacterium. We present here the complete genome sequence of P. aroidearum L6. The L6 strain carries a single 4,995,896-bp chromosome with 53.10% G + C content and harbors 4,306 predicted protein-coding genes. We estimated in silico DNA–DNA hybridization and average nucleotide identity values in combination with the whole-genome-based phylogeny from 19 Pectobacterium strains including P. aroidearum L6. The results showed that L6 and PC1 formed a population distinct from other populations of the Pectobacterium genus. Phylogenetic analysis based on 16S rRNA and genome sequences showed a close evolutionary relationship among Pectobacterium species. Overall, evolutionary analysis showed that L6 was in the same branch with PC1. In comparison with 18 Pectobacterium spp. reference pathogens, strain L6 had 2,712 gene families, among which 1,632 gene families were identified as orthologous to those strains, as well as 1 putative unique gene family. We discovered 478 genes, 10.4% of the total of predicted genes, that were potentially related to pathogenesis using the Virulence Factors of Pathogenic Bacteria database. A total of 25 genes were related to toxins, 35 encoded plant cell-wall degrading enzymes, and 122 were involved in secretion systems. This study provides a foundation for a better understanding of the genomic structure of P. aroidearum and particularly offers information for the discovery of potential pathogenic factors and the development of more effective strategies against this pathogen.

Comparative Genomic Analysis of Pathogenic Factors of Pectobacterium Species Isolated in South Korea Using Whole-Genome Sequencing

“…Six Ppa strains, including type strains, also did not demonstrate T1SSa similar to HC, and three subsets have been identified in Pectobacterium species ( Li et al, 2018 ). In other studies, P. aroidearum strain L6 showed 14 genes, and P. aroidearum strain PC1 demonstrated one gene ( He et al, 2021 ; Xu et al, 2021 ). Further study on T1SS and protease secretion is required since Ppa strains, including HC with three T1SS, did not show protease activity in the medium ( Jee et al, 2020 ).…”

“…MYP201603 had more functional genes in 11 groups. P. aroidearum L6 was different in three COGs groups including the defense mechanisms group (V), the cell motility group (N), and the signal transduction mechanisms group (T) ( Xu et al, 2021 ). The Pba strain SX309 differed from HNP201719 in the N group and the T group ( Li et al, 2019 ).…”

“…T2SS was identified to be highly conserved in this study, similar to other studies ( Li et al, 2018 , 2019 ). Xu et al (2021) reported 23 genes with loss of gspS in the T2SS of strain L6. This conservation could be attributed to the importance of T2SS, which secretes extracellular PCWDEs used as the main weapon by Pectobacterium .…”

Identification of new Dickeya dadantii virulence factors secreted by the type 2 secretion system

“…It is tempting to speculate that the presence/absence of these proteins could influence the host preference of some Dickeya species, providing additional virulence factors favorable to infect certain hosts. Works that compare Dickeya strains to understand what makes difference in their host range or aggressivity often focus only on the presence of the six known types of secretion systems without analyzing what proteins could be secreted [ 20 , 38 , 39 ]. An exhaustive analysis of the secreted proteins would be more informative.…”

Whole Genome Sequencing and Annotation of Naematelia aurantialba (Basidiomycota, Edible-Medicinal Fungi)

“…The CD-HIT rapid clustering of similar protein software was used to analyze the core pan of N. aurantialba with several typical basidiomycetes. Previous studies on the core-pan analysis were mostly done at the genus or family level because the only strains in the same genus or even family as N. aurantialba that have been sequenced are N. encephala, so the eight most typical basidiomycetes were selected and core-pan analysis was performed at the class level to investigate functional differences and similarities among the strains [87][88][89].…”