Evolution of the Core Genome of Pseudomonassyringae , a Highly Clonal, Endemic PlantPathogen

Abstract

Pseudomonas syringae is a common foliar bacterium responsible for many important plant diseases. We studied the population structure and dynamics of the core genome of P. syringae via multilocus sequencing typing (MLST) of 60 strains, representing 21 pathovars and 2 nonpathogens, isolated from a variety of plant hosts. Seven housekeeping genes, dispersed around the P. syringae genome, were sequenced to obtain 400 to 500 nucleotides per gene. Forty unique sequence types were identified, with most strains falling into one of four major clades. Phylogenetic and maximum-likelihood analyses revealed a remarkable degree of congruence among the seven genes, indicating a common evolutionary history for the seven loci. MLST and population genetic analyses also found a very low level of recombination. Overall, mutation was found to be approximately four times more likely than recombination to change any single nucleotide. A skyline plot was used to study the demographic history of P. syringae. The species was found to have maintained a constant population size over time. Strains were also found to remain genetically homogeneous over many years, and when isolated from sites as widespread as the United States and Japan. An analysis of molecular variance found that host association explains only a small proportion of the total genetic variation in the sample. These analyses reveal that with respect to the core genome, P. syringae is a highly clonal and stable species that is endemic within plant populations, yet the genetic variation seen in these genes only weakly predicts host association.

A User's Guide to a Data Base of the Diversity of Pseudomonas syringae and Its Application to Classifying Strains in This Phylogenetic Complex

“…S1a) and genetic distances among the strains (Table S7). A genetic distance between concatenated sequences of less than 5% defined clearly the seven previously described phylogroups: phylogroups 1, 2 and 3 [29], phylogroup 4 [15], phylogroup 5 [16] and phylogroups 6 and 7 [4]. We used the same distance threshold of 5% for the delimitations of additional phylogroups (Table S7, Fig.…”

Type III Effector Diversification via Both Pathoadaptation and Horizontal Transfer in Response to a Coevolutionary Arms Race

“…syringae strains isolated worldwide from ∼40 plant hosts. All 96 strains were phylogenetically characterized via multilocus sequence typing (MLST) [40] of the core genome to determine their clonal evolutionary relationships. Both Southern hybridization using T3SE probes and PCR were used to determine the distribution of the HopZ family members.…”

“…Forty-two isolates, distributed throughout all five P. syringae phylogroups [40], were positive for at least one effector (Figure 2). Promoter analysis, RT-PCR, and northern blot analysis (Figure S1) confirmed that a total of 39 isolates from 18 different hosts express hopZ , with 16 strains expressing hopZ1 , 13 expressing hopZ2 , and ten expressing hopZ3 .…”

“…The host of isolation is presented to the right of each strain. See [40,65] and Table S1 for details. Black squares represent presence of the corresponding gene, whereas white ones represent absence.…”

Multilocus Sequence Typing Reveals Relevant Genetic Variation and Different Evolutionary Dynamics among Strains of Xanthomonas arboricola pv. juglandis

“…Establishing different kinds of strain evolution (i.e., diversifying, directional, purifying) is a fundamental prerequisite for better understanding the epidemiology and the cycle of disease of the pathogen [12]. So far, the studies concerning MLST analysis and plant pathogenic bacteria revealed that Xylella fastidiosa, the Pseudomonas syringae complex and the "core" genome of Ralstonia solanacearum have a clonal structure [12][13][14], whereas in the pathogenicity islands, in gyrB and in four other gene fragments of P. viridiflava, in gyrB and rpoD of P. syringae pv. Tomato, as well as in the virulence-related egI and hrpB genes of R. solanacearum, recombination contributed more than mutation to the genetic variability among strains [12,15,16].…”