Comparative genomics and pathogenicity potential of members of the Pseudomonas syringae species complex on Prunus spp

Abstract

Background Diseases on Prunus spp. have been associated with a large number of phylogenetically different pathovars and species within the P. syringae species complex. Despite their economic significance, there is a severe lack of genomic information of these pathogens. The high phylogenetic diversity observed within strains causing disease on Prunus spp. in nature, raised the question whether other strains or species within the P. syringae species complex were potentially pathogenic on Prunus spp. Results To gain insight into the genomic potential of adaptation and virulence in Prunus spp., a total of twelve de novo whole genome sequences of P. syringae pathovars and species found in association with diseases on cherry (sweet, sour and ornamental-cherry) and peach were sequenced. Strains sequenced in this study covered three phylogroups and four clades. These strains were screened in vitro for pathogenicity on Prunus spp. together with additional genome sequenced strains thus covering nine out of thirteen of the currently defined P. syringae phylogroups. Pathogenicity tests revealed that most of the strains caused symptoms in vitro and no obvious link was found between presence of known virulence factors and the observed pathogenicity pattern based on comparative genomics. Non-pathogenic strains were displaying a two to three times higher generation time when grown in rich medium. Conclusion In this study, the first set of complete genomes of cherry associated P. syringae strains as well as the draft genome of the quarantine peach pathogen P. syringae pv. persicae were generated. The obtained genomic data were matched with phenotypic data in order to determine factors related to pathogenicity to Prunus spp. Results of this study suggest that the inability to cause disease on Prunus spp. in vitro is not the result of host specialization but rather linked to metabolic impairments of individual strains. Electronic supplementary material The online version of this article (10.1186/s12864-019-5555-y) contains supplementary material, which is available to authorized users.

Diversity of pathogenic Pseudomonas isolated from citrus in Tunisia

“…The citrus- P. syringae pathosystem is complex as shown previously on Prunus species. Ruinelli et al ( 2019 ) found that a large number of various P. syringae strains are pathogenic on the tested hosts (cherry, peach and almond). Similarly Parisi et al ( 2019 ), isolated four phylogroups (PG01, 02, 03 and 07) able to induce canker on apricot.…”

“…Similarly Parisi et al ( 2019 ), isolated four phylogroups (PG01, 02, 03 and 07) able to induce canker on apricot. Ruinelli et al ( 2019 ) suggest the diversity of strains pathogenic on Prunus is probably due to independent evolution of individual strains, not necessarily related to virulence.…”

“…It seems that many Pseudomonas species could be involved in citrus blast and black pit and that these diseases are more complex than previously thought. In order to better understand the situation in Tunisian orchards, Oueslati et al ( 2019 ), using a similar approach, identified two new pathogenic Pseudomonas species involved in citrus black pit disease in different Tunisian sites: P. kairouanensis and P. nabeulensis . In this study, we aimed to explore the diversity and population structure of the pathogenic bacteria from the P. syringae group on citrus in Tunisia.…”

Cherry picking by pseudomonads: After a century of research on canker, genomics provides insights into the evolution of pathogenicity towards stone fruits

“…Significantly, sampling studies have indicated that the different pathogens commonly coexist within orchards, nurseries, and forests (Vicente et al, 2004;Gilbert et al, 2008;Kałużna et al, 2010). (Gilbert et al, 2008;Bultreys and Kałużna, 2010;Hulin et al, 2018a;Parisi et al, 2019;Ruinelli et al, 2019). Psm R1 and R2 have evolved within woody host-infecting clades of phylogroups 3 and 1, respectively (Nowell et al, 2016).…”

“…To understand how each of the different clades have evolved virulence on cherry, genomic analysis allowed the identification of the sets of genes encoding T3Es and toxin and hormone biosynthesis (Hulin et al, 2018a;Ruinelli et al, 2019;Marcelletti and Scortichini, 2019).…”