Comparative genomic insights into the epidemiology and virulence of plant pathogenic pseudomonads from Turkey

Abstract

Pseudomonas is a highly diverse genus that includes species that cause disease in both plants and animals. Recently, pathogenic pseudomonads from the Pseudomonas syringae and Pseudomonas fluorescens species complexes have caused significant outbreaks in several agronomically important crops in Turkey, including tomato, citrus, artichoke and melon. We characterized 169 pathogenic Pseudomonas strains associated with recent outbreaks in Turkey via multilocus sequence analysis and whole-genome sequencing, then used comparative and evolutionary genomics to characterize putative virulence mechanisms. Most of the isolates are closely related to other plant pathogens distributed among the primary phylogroups of P. syringae , although there are significant numbers of P. fluorescens isolates, which is a species better known as a rhizosphere-inhabiting plant-growth promoter. We found that all 39 citrus blast pathogens cluster in P. syringae phylogroup 2, although strains isolated from the same host do not cluster monophyletically, with lemon, mandarin orange and sweet orange isolates all being intermixed throughout the phylogroup. In contrast, 20 tomato pith pathogens are found in two independent lineages: one in the P. syringae secondary phylogroups, and the other from the P. fluorescens species complex. These divergent pith necrosis strains lack characteristic virulence factors like the canonical tripartite type III secretion system, large effector repertoires and the ability to synthesize multiple bacterial phytotoxins, suggesting they have alternative molecular mechanisms to cause disease. These findings highlight the complex nature of host specificity among plant pathogenic pseudomonads.

Dressing like a pathogen: Comparative analysis of different Pseudomonas genomospecies wearing different features to infect Corylus avellana

“…The canonical tripartite TPAI is present in Pseudomonas syringae strains of phylogroup 1, 2, 3, 4, 5, 6 and 10, together with an additional genomic island Rhizobium (RPAI) system present in some P. syringae of phylogroups 2 and 3. Phylogroups 7 and 11 are carrying the Single Pathogenicity Island (SPAI), while the fluorescence (FPAI) system and corrugata (CPAI) island are present only in Pseudomonas fluorescence species complex and Pseudomonas corrugata , respectively (Dillon et al, 2021). The presence of the tripartite mosaic structure codifying for the type III secretion system was confirmed in all the 23 strains under study, together with an additional genomic island of 20 Kb identified as the Rhizobium (RPAI) system (Dillon et al, 2021).…”

“…Phylogroups 7 and 11 are carrying the Single Pathogenicity Island (SPAI), while the fluorescence (FPAI) system and corrugata (CPAI) island are present only in Pseudomonas fluorescence species complex and Pseudomonas corrugata , respectively (Dillon et al, 2021). The presence of the tripartite mosaic structure codifying for the type III secretion system was confirmed in all the 23 strains under study, together with an additional genomic island of 20 Kb identified as the Rhizobium (RPAI) system (Dillon et al, 2021). This region was only of 10Kb in Pav MAFF 212061 and totally absent in Pav CC1416 and Pss CRAFRU11 (Figure 5).…”

“…On the contrary, HopE1 may be specific for Prunus infection. Besides the canonical tripartite pathogenicity island (TPAI), all the strains except for Pav CC1416 and Psav CRAFRU11 contain an additional genomic island Rhizobium (RPAI) system, as previously described by Dillon et al (2021) for other Pseudomonas . This island of about 20Kb is most likely the same identified by Marcelletti and Scortichini (2015) in the nine pseudomonads infecting European hazelnut trees.…”

“…As proved here, this genomic region may not be involved in host‐specificity since it is present in all the strains. On the contrary, phytotoxins may play a pivotal role in the evolution of host specificity, since they particularly counteract the immunity response (Dillon et al, 2021). The phytotoxins are more specific for the syringae group, which all contain the complete Mbo and Mgo operons for the mangotoxin production, necessary for mango necrosis, as well as a complete ice nucleation cluster (Marcelletti & Scortichini, 2015).…”

“…morsprunorum race 2, have been isolated from Prunus avium as well (Hulin et al, 2018, 2020). This apparent contradiction could be explained by the observation that the host‐range determinants of Pseudomonas selectivity are mainly linked to virulence‐related factors like the type III secretion system and their relative secreted effectors, phytotoxins, WHOP (Woody hosts and Pseudomonas ) and woody associated enzymes, as reported in a recent study by Dillon et al (2021).…”