Pseudomonas syringae pv. tomato strain DC3000 (PtoDC3000) is one of the most intensively studied bacterial plant pathogens today. Here we report a thorough investigation into PtoDC3000 and close relatives isolated from Antirrhinum majus (snapdragon), Apium graveolens (celery), and Solanaceae and Brassicaceae species. Multilocus sequence typing (MLST) was used to resolve the precise phylogenetic relationship between isolates and to determine the importance of recombination in their evolution. MLST data were correlated with an analysis of the locus coding for the type III secreted (T3S) effector AvrPto1 to investigate the role of recombination in the evolution of effector repertoires. Host range tests were performed to determine if closely related isolates from different plants have different host ranges. It was found that PtoDC3000 is located in the same phylogenetic cluster as isolates from several Brassicaceae and Solanaceae species and that these isolates have a relatively wide host range that includes tomato, Arabidopsis thaliana, and cauliflower. All other analyzed tomato isolates from three different continents form a distinct cluster and are pathogenic only on tomato. Therefore, PtoDC3000 is a very unusual tomato isolate. Several recombination breakpoints were detected within sequenced gene fragments, and population genetic tests indicate that recombination contributed more than mutation to the variation between isolates. Moreover, recombination may play an important role in the reassortment of T3S effectors between strains. The data are finally discussed from a taxonomic standpoint, and P. syringae pv. tomato is proposed to be divided into two pathovars.Pseudomonas syringae pv. tomato DC3000 (PtoDC3000) is one of the most intensively studied plant pathogen isolates today. It was completely sequenced (6), and a large part of what is known about the plant immune system has been learned by studying the interaction of PtoDC3000 with its hosts Arabidopsis thaliana and tomato (Solanum lycopersicum), as can be seen from many recent high-profile publications (see references 39 and 47 for examples). However, much less is known about how PtoDC3000 relates to other P. syringae strains. Although PtoDC3000 is a rifampin-resistant derivative of the type strain of P. syringae pv. tomato (9; D. Cuppels, personal communication), its host range (which includes tomato, cauliflower [Brassica oleracea var. botrytis], and A. thaliana) was found to be more similar to that of pathovar maculicola isolates from Brassicaceae species than to the host range of other P. syringae pv. tomato strains (which are limited to tomato) (10, 58). Also, based on physiological (10) and molecular analyses (10, 63), PtoDC3000 was suggested to be more similar to pathovar maculicola strains than to other pathovar tomato strains. However, since strains of pathovars tomato, maculicola, antirrhini (isolated from ornamental snapdragon, Antirrhinum majus), and apii (isolated from celery, Apium graveolens) were all found to be closely related (18, 25), the...

Pseudomonas syringae causes plant diseases, and the main virulence mechanism is a type III secretion system (T3SS) that translocates dozens of effector proteins into plant cells. Here we report the existence of a subgroup of P. syringae isolates that do not cause disease on any plant species tested. This group is monophyletic and most likely evolved from a pathogenic P. syringae ancestor through loss of the T3SS. In the nonpathogenic isolate P. syringae 508 the genomic region that in pathogenic P. syringae strains contains the hrp-hrc cluster coding for the T3SS and flanking effector genes is absent. P. syringae 508 was also surveyed for the presence of effector orthologues from the closely related pathogenic strain P. syringae pv. syringae B728a, but none were detected. The absence of the hrp-hrc cluster and effector orthologues was confirmed for other nonpathogenic isolates. Using the AvrRpt2 effector as reporter revealed the inability of P. syringae 508 to translocate effectors into plant cells. Adding a plasmid-encoded T3SS and the P. syringae pv. syringae 61 effector gene hopA1 increased in planta growth almost 10-fold. This suggests that P. syringae 508 supplemented with a T3SS could be used to determine functions of individual effectors in the context of a plant infection, avoiding the confounding effect of other effectors with similar functions present in effector mutants of pathogenic isolates.Pseudomonas syringae is probably the most intensively studied bacterial plant pathogen for which molecular interactions with host and nonhost plants have been dissected in great detail (16,43,50). P. syringae is a member of the Gammaproteobacteria and comprises strains isolated from dozens of cultivated, ornamental, and wild plants. According to the current taxonomy, isolates are grouped into different pathovars based on the plant host from which they were isolated (65). The diseases that P. syringae strains cause range from foliar spot diseases to blights, stripes, and cankers (1). Bacteria are transmitted mainly by rain and wind, can survive for periods of time on leaf surfaces as epiphytes without causing disease, and then enter leaves either through natural openings like stomata or through wounds and finally reach high population densities in the intercellular plant spaces and cause visible disease symptoms (26). Recently, P. syringae isolates have been found in clouds, rain, snow, and river epilithion, suggesting that these environments are important inoculum sources (44).P. syringae is able to cause diseases in its hosts because of its ability to suppress plant defenses elicited by microbe-associated molecular patterns (MAMPs) or pathogen-associated molecular patterns (PAMPs) like flagellin (23). These defenses are called PAMP-triggered immunity (PTI) (11). Suppression of PTI is accomplished by effector proteins that are translocated from P. syringae into plant cells by means of a type III secretion system (T3SS) and by toxins (for example, coronatine) (38, 43). However, on some plants, effectors are directl...

Wheat Gli-2 loci encode complex groups of α-gliadin prolamins that are important for breadmaking, but also major triggers of celiac disease (CD). Elucidation of α-gliadin evolution provides knowledge to produce wheat with better end-use properties and reduced immunogenic potential. The Gli-2 loci contain a large number of tandemly duplicated genes and highly repetitive DNA, making sequence assembly of their genomic regions challenging. Here, we constructed high-quality sequences spanning the three wheat homeologous α-gliadin loci by aligning PacBio-based sequence contigs with BioNano genome maps. A total of 47 α-gliadin genes were identified with only 26 encoding intact full-length protein products. Analyses of α-gliadin loci and phylogenetic tree reconstruction indicate significant duplications of α-gliadin genes in the last ~2.5 million years after the divergence of the A, B and D genomes, supporting its rapid lineage-independent expansion in different Triticeae genomes. We showed that dramatic divergence in expression of α-gliadin genes could not be attributed to sequence variations in the promoter regions. The study also provided insights into the evolution of CD epitopes and identified a single indel event in the hexaploid wheat D genome that likely resulted in the generation of the highly toxic 33-mer CD epitope.