Pseudomonas syringae Genomics: From Comparative Genomics of Individual Crop Pathogen Strains Toward Population Genomics
Whole-genome sequencing has become so affordable that we can now sequence genomes of dozens of individuals of a pathogen population instead of sequencing a single representative isolate. This change of framework enables us to answer questions impossible t
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Pseudomonas syringae Genomics: From Comparative Genomics of Individual Crop Pathogen Strains Toward Population Genomics Boris A. Vinatzer and Caroline L. Monteil
4.1
Who Is Pseudomonas syringae
Pseudomonas syringae sensu lato is a species that includes a genetically and phenotypically diverse group of Gammaproteobacteria, whose exact taxonomic status is still in flux. This group includes a few dozen causative agents of economically important crop diseases and a large number of genetically distinct strains isolated from wild plants, leaf litter, and compartments of the water cycle (e.g., clouds, precipitation, snowpack, lakes, and rivers) (Morris et al. 2008, 2010, 2013; Monteil et al. 2012). The named species most closely related to P. syringae are P. cichorii (Swingle 1925) and P. viridiflava (Burkholder 1930), which were originally described as species separate from P. syringae sensu stricto (Van Hall 1904) because of distinguishable phenotypic characteristics compared to P. syringae sensu stricto. Interestingly, even considering only crop pathogens, strains related to the P. syringae-type strain could be assigned to nine different species based on DNA similarity (or better dissimilarity). However,
B. A. Vinatzer (&) C. L. Monteil Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA, USA e-mail: [email protected] C. L. Monteil INRA, UR0407 Pathologie Végétale, 84143, Montfavet cedex, France
since no consistent phenotypic characteristics distinguish these nine groups, most of these groups could not be described as named species and are thus referred to as numbered ‘‘genomospecies’’ 1 through 9 (Gardan et al. 1999). It was recently shown that each genomospecies corresponds to a phylogenetic group (Bull et al. 2011) based on multilocus sequence typing (MLST) (Maiden et al. 1998). Each genomospecies of P. syringae gathers different crop pathogens that are described based on their host range and the type of disease symptoms they cause. They are referred to as ‘‘pathovars’’ (Dye et al. 1980), and each pathovar is represented by a pathotype strain similar to type strains of named species. However, many genetic lineages of P. syringae have not been assigned to pathovars because either they did not cause disease on any tested plant species (Clarke et al. 2010) or simply because they were isolated from non-plant substrates and have not been tested for host range. They are currently simply assigned to phylogenetic groups based on MLST building on the MLST scheme originally developed by Sarkar and Guttman (2004). While Chap. 3 describes and compares genomes of relatively distantly related strains belonging to different pathovars—or even different genomospecies—in this chapter, we will focus on how genome sequencing of very closely related strains belonging to the same phylogenetic group—or even the same pathovar—has started to give insight into various aspects of pathogen emergence, evolution, molecular
D. C. Gross et al. (eds.), Genomics of Plant-Associa
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