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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.
Highlights
Soft rot Pectobacteriaceae are considered to be one of the top ten most important agricultural phytopathogens (Mansfield et al, 2012)
P. carotovorum subsp. carotovorum tends to serve as a catchall for pectobacteria isolates differing from the specific descriptions of the other pectobacteria taxa, and P. aroidearum was classified as a novel species in 2013 (Nabhan et al, 2013)
GC-Depth analysis was performed on the assembly results to show the assembly length (4,995,896 bp), coverage length (4,995,089), coverage (99.98%), reads usage percent (95.3%), and depth (260) of P. aroidearum L6
Summary
Soft rot Pectobacteriaceae are considered to be one of the top ten most important agricultural phytopathogens (Mansfield et al, 2012). Hauben et al (1998) established the genus Pectobacterium that included three species and five subspecies: P. cacticidum, P. chrysanthemi, P. cypripedii, P. carotovorum subsp. Three subspecies of P. carotovorum were elevated into the species level, namely P. atrosepticum, P. odoriferum, and P. wasabiae (Gardan et al, 2003; Duarte et al, 2004; Nykyri et al, 2012). The classification of the genus Pectobacterium has been subjected to wide revision over the last decade, and it is likely that some of the genomesequenced strains have been incorrectly assigned to P. carotovorum (Gardan et al, 2003; Khayi et al, 2016; Pritchard et al, 2016; Zhang et al, 2016). The genome-sequenced strain PC1 (formerly classified as P. carotovorum subsp. carotovorum) is P. aroidearum under the new classification (Nabhan et al, 2013)
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