Abstract
A recent re-emerging bacterial canker disease incited by Pseudomonas syringae pv. actinidiae (Psa) is causing severe economic losses to Actinidia chinensis and A. deliciosa cultivations in southern Europe, New Zealand, Chile and South Korea. Little is known about the genetic features of this pathovar. We generated genome-wide Illumina sequence data from two Psa strains causing outbreaks of bacterial canker on the A. deliciosa cv. Hayward in Japan (J-Psa, type-strain of the pathovar) and in Italy (I-Psa) in 1984 and 1992, respectively as well as from a Psa strain (I2-Psa) isolated at the beginning of the recent epidemic on A. chinensis cv. Hort16A in Italy. All strains were isolated from typical leaf spot symptoms. The phylogenetic relationships revealed that Psa is more closely related to P. s. pv. theae than to P. avellanae within genomospecies 8. Comparative genomic analyses revealed both relevant intrapathovar variations and putative pathovar-specific genomic regions in Psa. The genomic sequences of J-Psa and I-Psa were very similar. Conversely, the I2-Psa genome encodes four additional effector protein genes, lacks a 50 kb plasmid and the phaseolotoxin gene cluster, argK-tox but has acquired a 160 kb plasmid and putative prophage sequences. Several lines of evidence from the analysis of the genome sequences support the hypothesis that this strain did not evolve from the Psa population that caused the epidemics in 1984–1992 in Japan and Italy but rather is the product of a recent independent evolution of the pathovar actinidiae for infecting Actinidia spp. All Psa strains share the genetic potential for copper resistance, antibiotic detoxification, high affinity iron acquisition and detoxification of nitric oxide of plant origin. Similar to other sequenced phytopathogenic pseudomonads associated with woody plant species, the Psa strains isolated from leaves also display a set of genes involved in the catabolism of plant-derived aromatic compounds.
Highlights
Pseudomonas syringae is a worldwide phytopathogenic microorganism mainly adapted to plant species, both monocotyledon and dicotyledon, and either cultivated or grown in wild habitats
Genome-wide sequence data We generated genome-wide Illumina IIx sequence data from one strain of Psa isolated in Japan, NCPPB3739 ( = KW 11) which is the type-strain of the pathovar and here referred to as J-Psa, and two Psa strains from Italy, NCPPB3871 and CRA-FRU 8.43, which were isolated during two different outbreaks of bacterial canker on Actinidia species and here referred to as I-Psa and I2-Psa, respectively
This study has determined putative variable genomic regions and sets of genes related to the pathogenicity and virulence that could differentially modulate the aggressiveness of pathogen populations towards Actinidia species as well as genes involved in the environmental fitness and adaptation of the bacterium in planta
Summary
Pseudomonas syringae is a worldwide phytopathogenic microorganism mainly adapted to plant species, both monocotyledon and dicotyledon, and either cultivated or grown in wild habitats. The most common symptoms of P. syringae include leaf spots and necrosis, fruit specks and scabs, flower wilting, twig die-back, branch and trunk cankers and, in particular circumstances, plant death [5]. On the basis of visually assessed symptoms and host range tests and with the aid of biochemical, physiological and nutritional tests and molecular typing, P. syringae (i.e. the P. syringae species complex) is divided into 57 pathovars [6]. To genetically circumscribe 48 P. syringae pathovars and some related species of phytopathogenic pseudomonads, Gardan et al, [7] performed DNA-DNA hybridisation and ribotyping analyses and pointed out nine discrete genomospecies. By performing repetitive-sequence PCR, ARDRA and AFLP analyses, this pathovar was subsequently placed into genomospecies 8 together with P. avellanae and P. s. By performing repetitive-sequence PCR, ARDRA and AFLP analyses, this pathovar was subsequently placed into genomospecies 8 together with P. avellanae and P. s. pv. theae [8,9]
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