To gain insights into the diversity of
Pseudomonas syringae
sensu lato affecting sweet cherry in California, we sequenced and analyzed the phylogenomic and genomic architecture of 86 fluorescent pseudomonads isolated from symptomatic and asymptomatic cherry tissues. Fifty-eight isolates were phylogenetically placed within the
P. syringae
species complex and taxonomically classified into five genomospecies:
P. syringae
pv.
syringae
,
P. syringae
,
Pseudomonas cerasi
,
Pseudomonas viridiflava
, and
A
. We annotated components of the type III secretion system and phytotoxin-encoding genes and correlated the data with pathogenicity phenotypes. Intact probable regulatory protein HrpR was annotated in the genomic sequences of all isolates of
P. syringae
pv.
syringae
,
P. syringae
,
P. cerasi
, and
A
. Isolates of
P. viridiflava
had atypical probable regulatory protein HrpR. Syringomycin and syringopeptin-encoding genes were annotated in isolates of all genomospecies except for
A
and
P. viridiflava
. All isolates of
P. syringae
pv.
syringae
caused cankers, leaf spots, and fruit lesions in the field. In contrast, all isolates of
P. syringae
and
P. cerasi
and some isolates of
P. viridiflava
caused only cankers. Isolates of genomospecies
A
could not cause any symptoms suggesting phytotoxins are essential for pathogenicity. On detached immature cherry fruit pathogenicity assays, isolates of all five genomospecies produced symptoms (black–dark brown lesions). However, symptoms of isolates of genomospecies
A
were significantly (
P
< 0.01) less severe than those of other genomospecies. We also mined for genes conferring resistance to copper and kasugamycin and correlated these data with
in vitro
antibiotic sensitivity tests.
IMPORTANCE
Comprehensive identification of phytopathogens and an in-depth understanding of their genomic architecture, particularly virulence determinants and antibiotic-resistant genes, are critical for several practical reasons. These include disease diagnosis, improved knowledge of disease epidemiology, pathogen diversity, and determination of the best possible management strategies. In this study, we provide the first report of the presence and pathogenicity of genomospecies
Pseudomonas cerasi
and
Pseudomonas viridiflava
in California sweet cherry. More importantly, we report a relatively high level of resistance to copper among the population of
Pseudomonas syringae
pv.
syringae
(47.5%). This implies copper cannot be effectively used to control bacterial blast and bacterial canker of sweet cherries. On the other hand, no isolates were resistant to kasugamycin, an indication that kasugamycin could be effectively used for the control of bacterial blast and bacterial canker. Our findings are important to improve the management of bacterial blast and bacterial canker of sweet cherries in California.