Whole genome sequencing revealed the presence of a genomic anomaly in the region of 4.7 to 4.9 Mb of the Pseudomonas syringae pv. tomato (Pst) DC3000 genome. The average read depth coverage of Pst DC3000 whole genome sequencing results suggested that a 165 kb segment of the chromosome had doubled in copy number. Further analysis confirmed the 165 kb duplication and that the two copies were arranged as a direct tandem repeat. Examination of the corresponding locus in Pst NCPPB1106, the parent strain of Pst DC3000, suggested that the 165 kb duplication most likely formed after the two strains diverged via transposition of an ISPsy5 insertion sequence (IS) followed by unequal crossing over between ISPsy5 elements at each end of the duplicated region. Deletion of one copy of the 165 kb region demonstrated that the duplication facilitated enhanced growth in some culture conditions, but did not affect pathogenic growth in host tomato plants. These types of chromosomal structures are predicted to be unstable and we have observed resolution of the 165 kb duplication to single copy and its subsequent re-duplication. These data demonstrate the role of IS elements in recombination events that facilitate genomic reorganization in P. syringae.
Citation: Bao Z, Stodghill PV, Myers CR, Lam H, Wei H-L, Chakravarthy S, et al. (2014) Genomic Plasticity Enables Phenotypic Variation of Pseudomonas syringae pv. tomato DC3000. PLoS ONE 9(2): e86628. https://doi.org/10.1371/journal.pone.0086628
Editor: Dawn Arnold, University of the West of England, United Kingdom
Received: October 29, 2013; Accepted: December 16, 2013; Published: February 6, 2014
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
Funding: This work was funded by the USDA-ARS. This work was partially supported by National Science Foundation Plant Genome Research Program Grant IOS-1025642. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Genetic diversity within populations underpins the process of natural selection, enabling individuals with particular genotypes to outgrow competitors, survive stresses and invade or specialize for growth in different environments. Unlike eukaryotes that have the benefit of meiotic recombination, genetic variation in prokaryotes is not mechanistically tied with reproduction, but instead, is achieved through horizontal transfer , , , , mutation ,  and recombination , , , . This strategy works for prokaryotes because their unicellular nature allows genetic diversity to arise within a population and for natural selection to act upon each cell, permitting evolution to advance by directly selecting the fittest individuals from the population .
Plant pathogenic bacteria have adapted to the specific challenges associated with invading and colonizing plant tissues. In most plant pathogenic bacteria the pathogenic process involves Type Three secretion system-dependent injection of virulence effectors into host cells, which interfere with the plant's ability to detect infection and disrupt the plant's immune defenses . Colonization and disease depend on the bacteria injecting the correct combination of effectors that prevent or suppress the plant's defenses without provoking an unchecked immune response. The relationship between bacterial virulence mechanisms and plant immune systems can be portrayed as an evolutionary arms race, in which the plant immune and microbe virulence systems continuously adapt to each other .
Pseudomonas syringae is a complex of Gram-negative γ-proteobacteria that exist in diverse environments and cause disease in many plants . P. syringae is divided into more than 50 distinct pathovars  and further subdivided into races based on the range of host species and cultivars that individual strains can infect. Host specificity is partially determined by the combination of effectors produced, and can change by altering the effector gene repertoire , . Furthermore, it now appears that wild (non-domesticated) populations of P. syringae may exist as generalists and adapt away from this lifestyle to specialize as aggressive host-specific pathogens in agricultural monoculture systems . In the process of adapting to new hosts, the bacteria may be exposed to antimicrobial plant defenses that select for mutants with compatible effector repertoires. The fastest mechanisms to permit adaptation involve recombination  and genomic rearrangement , in some cases mediated by transposition or other mobile DNA elements , , . These sorts of genomic events are much more frequent than beneficial point mutations ,  and allow the organism to make evolutionary leaps, changing phenotypes dramatically in a single event , .
Several P. syringae strains have emerged as tractable models used extensively to investigate the molecular mechanisms of plant-microbe interactions , , . One widely used model strain is P. syringae pv. tomato (Pst) DC3000, the first member of the P. syringae group for which a complete, closed genome sequence was reported . Here we identify and characterize a dynamic, 165 kb genomic duplication in Pst DC3000 that can influence growth of the bacteria in different conditions. We used whole genome sequence-assisted copy number analysis to identify the 165 kb duplicated region, and determined the structural organization and genomic location using PCR and recombineering. Our results show that this duplication is present in some laboratory isolates including the Pst DC3000 isolate used to produce the reference sequence  and in the Pst DC3000 strain commercially available from the American Type Culture Collection (ATCC). However, the 165 kb duplication is not present in Pst NCPPB1106, the strain from which Pst DC3000 is derived, indicating that the duplication arose after the two strains diverged in the mid-1980's , . The 165 kb duplication has the structure of a typical tandem repeat  in which each copy is separated from the other and flanked on each end by an ISPsy5 insertion sequence (IS). These observations provide evidence that homologous recombination between identical IS elements can facilitate genomic flexibility in Pst DC3000 and suggest a mechanism by which bacteria can adapt to diverse and changing environments.
Materials and Methods
Bacterial strains and growth conditions
P. syringae strains (Table 1) were grown at 28°C in Kings B (KB) medium  or on KB medium solidified with 1.5% (wt/vol) agar. Rifampicin, gentamycin, kanamycin, and tetracycline were used at 50 µg/ml, 10 µg/ml, 50 µg/ml and 10 µg/ml respectively. Escherichia coli DH5α was used as the host for subcloning and other plasmid manipulations. E. coli was grown at 37°C in LB medium or LB medium solidified with 1.5% (wt/vol) agar.
The Pst DC3000(D28EΔiaaL) strain was constructed by deletion of the iaaL gene from Pst DC3000(D28E)  using marker exchange mutagenesis , . The locus tag for the iaaL gene is PSPTO_0371. The deletion construct was generated by cloning 1.2 kb left and 1.3 kb right flanking regions of PSPTO_0371 into pK18mobSacB as described previously . The two flanks were amplified from Pst DC3000 genomic DNA using primer pairs HL117/HL118 and HL119/HL120 (see Table S1 for all primer sequences), and then joined by SOEing PCR . The resulting 2.5 kb product was digested with XbaI and ligated with XbaI digested pK18mobsacB. The deletion construct was introduced into Pst DC3000(D28E) by electroporation and merodiploid intermediates were selected for growth on medium containing kanamycin. Recombinants that had eliminated pK18mobsacB plasmid sequences were identified by sucrose counter-selection. Sucrose-resistant, Km-sensitive colonies were screened by PCR using primer pair HL121/HL122. The mutation was confirmed by Sanger sequencing with primers HL121, HL122, HL123, HL124, HL161 and HL162.
For complementation, the iaaL gene was cloned into the P. syringae expression vector pBS46 for constitutive overexpression driven by the PnptII promoter. The iaaL gene from Pst DC3000 was cloned into pBS46 using Invitrogen Gateway cloning system as described in . The iaaL cloned in pENTR/SD/D was sequenced using primers shown in Table S1.
The structural organization of genomic loci was probed using PCR and Sanger sequencing. PCRs were carried out using Takara ExTaq premix. PCR products were resolved on 1% agarose gels, Roche DNA Molecular Weight Marker X was used to estimate length of PCR products. All Sanger sequencing was performed by the Cornell University Biotechnology Resource Center (BRC), Ithaca, NY.
Growth of P. syringae strains was analyzed in a Bioscreen automated growth curve analysis system. For these experiments, P. syringae strains were grown overnight at 30°C with vigorous shaking in liquid KB medium with appropriate antibiotics. The overnight cultures were diluted to OD600 of 0.2 and 200 µl the diluted overnights were cultured in the Bioscreen for 48 hours at 28°C with continuous shaking and OD600 measured every 15 minutes. Results shown are the average of three biological replicates.
Analysis of growth curves
The growth curve data for Pst DC3000 and Pst DC3000(dup165−) grown in KB were further analyzed to estimate the growth rates of each strain at early times during log phase. The growth curve data do not conform to simple mathematical models of bacterial growth , as there is no regime where bacterial growth is strictly exponential in time, as would be expected in log phase (see Figure S1). Nevertheless, both strains grew approximately exponentially at early times with instantaneous growth rates that remained in roughly constant proportion over the first 6 hours of growth. To quantitatively estimate a growth rate difference at early times, we performed the following analysis. First, taking the OD600 readings as proxy for the population size N in each sample, we normalized each growth curve by its initial population size N0 at time t = 0, and log-transformed the normalized data to obtain curves of log2(N/N0) vs t. The local slope of these log-transformed growth curves reflects the instantaneous growth rate at each point in time; we approximated the local slope numerically by computing a finite-difference approximation to the derivative of each curve at each time point (main part of Figure S1). Since computing finite-difference derivatives and ratios of data sets increases noise, we also repeated this same procedure with smoothed versions of the log-transformed growth data (boxcar window of width 10, red curve in inset), yielding an average growth rate ratio of 1.44±0.02. We thus estimate a 44% increase in growth rate for the wild-type Pst DC3000 strain at early times when both strains were growing approximately exponentially.
Sequencing and analysis
Whole genome sequencing was provided by the Cornell University BRC, Ithaca, NY. Library preparation and sequencing were performed according to the protocols provided by Illumina. The Pst DC3000(H0457), Pst DC3000(ATCC), Pst DC3000(ZB), Pst DC3000(LS), Pst DC3000(JB), Pst DC3000(BB), Pst DC3000(PS1) genomic DNA sequencing libraries were prepared using Illumina Genome Analyzer v4 sequencing kits, Genome Analyzer v4 cluster kits and sequenced on an Illumina Genome Analyzer GAIIx, using single-end 86 bp sequencing. Pst DC3000(D36E) and Pst DC3000(JF) genomic DNA sequencing libraries were prepared using Nextera XT DNA Sample Preparation Kit (24 samples, FC-131-1024) with Nextera XT Index Kit (FC-131-1001). The Pst NCPPB1106 genomic DNA sequencing libraries were prepared using Illumina TruSeq sample prep kit v2 and indexed with TruSeq indexed adaptor #1 (ATCACG). The Pst NCPPB1106, Pst DC3000(D36E) and Pst DC3000(JF) were sequenced using single-end 100 bp, using Illumina v3 cluster kits and SBS reagent kits on an Illumina HiSeq 2000, with HiSeq control software (HCS) version 184.108.40.206 and Real Time Analysis (RTA) software version 1.13.48.
Copy number analysis
Sinister profiles were constructed from raw high-throughput sequencing reads using the method described in , with the modification that the alignment was computed using Bowtie2 version 2.1.0  with the following non-default parameters, –local -L 31 –ma 1 –mp 3 –np 0 –rdg 2,3 –rfg 2,3 -k 2000 -i S,1,0.25 –score-min L,0,0.9. As described in , reads that could be aligned to multiple locations were discarded. We then computed a relative sequencibility score for each genomic position. We defined the relative sequencibility score for a base as the sequencibility score (N = 36)  for that base as a percentage of the maximum sequencibility score (e.g., if the sequencibility score is 30 out of 36, then the relative sequencibility score is 83%).
The positions in the genome were divided into non-overlapping windows of size 1000. All windows in which less than 80% of the bases had a relative sequencibility score of at least 90% were removed from further consideration.
For each of the remaining windows, we computed the average number of reads starting within that window (i.e., values in the sinister plot) for those bases with a relative sequencibility score of at least 90%. We used the log2 of the window average in the remainder of the analysis.
We observed that the read count varied across the genome as a result of replication. The closer to the origin, the larger the read count; the closer to the terminus, the lower. In order to account for this variation, we used the model described in , namely, that the read counts decrease exponentially as one moved farther from the origin and closer to the terminus. Thus in log-space the expected number of reads across the circular genome can be modeled by a pair of linear functions connecting the expected counts at the original with the expected counts at the terminus. We accounted for the observed variation across the genome in our analysis, as follows.
Using the method described above, we computed log2 averages for windows of lengths 1000 or 10,000 centered at the origin and at the terminus. We defined the expected counts across the circular genome as the two lines connecting these two values at these two locations. For each window, we then subtracted the expected read count average from the observed read count average.
In order to generate a list of regions of putative variable copy-number, we computed the mean and standard deviation for the corrected window averages. We declared any window average that was three standard deviations away from the global mean of correct averages to be an “outlier”, and an entry for that window was made in the output list (Table S2).
Recombineering was performed as described in . Recombineering substrates were produced by PCR and then 500 ng of DNA was used to transform the indicated P. syringae strains containing pUCP24/recTE by electroporation. The sequences of all oligos used are shown in Table S1. Oligos were purchased from Integrated DNA Technologies (IDT), Inc., Coralville, IA. PCR products were generated using ExTaq (Takara Bio, Inc, Japan) using the neo gene on pK18mobsacB  as the template. Fragment size of PCR generated substrates were confirmed by agarose gel electrophoresis and products were purified and concentrated by ethanol precipitation.
Plant virulence assays
Solanum lycopersicom ‘Moneymaker’ plants were germinated and grown in a greenhouse with approximate 16/8 light/dark cycles. Four to five week old plants were inoculated with 3×104 cfu/ml bacterial suspension using blunt syringe infiltration. Bacteria were recovered from plants by taking samples of the leaf tissue at the site of infection using a #2 disk punch (3 disks, total area 0.589 cm2) at 2 days post infection (dpi) and 5 dpi. Leaf disks were homogenized by mechanical disruption in 300 µl of 10 mM MgCl. Serial dilutions of the tissue homogenate were plated on the LM agar supplemented with rifampicin and the number of colony forming units per cm2 was calculated.
Identification of a cryptic duplication in the genome of Pst DC3000
ChIP-seq experiments conducted to identify several sigma factor regulons ,  serendipitously revealed evidence of an anomaly in the Pst DC3000 genome. Control samples used to demonstrate specific enrichment in these experiments suggested that a large segment of the Pst DC3000 genome had a higher than average copy number (Fig. S2). This motivated us to use Illumina methods to re-sequence Pst DC3000 used in our laboratories and align the results to the published Pst DC3000 reference sequence . The Pst DC3000 isolate sequenced in this experiment was prepared from the deep-frozen stock (storage no. H0457) that was cultured and sent by A. Collmer in June of 2000 to The Institute for Genomic Research (TIGR) where it was used to prepare genomic DNA for sequencing Pst DC3000 which was reported in Buell et al., 2003 .
The Illumina sequencing methods used here differ from Sanger sequencing in that the number of reads obtained are proportional to the relative amounts of input DNA. The results of Pst DC3000(H0457) re-sequencing were similar to what was observed in the ChIP-seq controls (above) and again showed a region in the vicinity of 4.7 to 4.9 Mbp of the Pst DC3000 genome sequence with increased read coverage (Fig. 1A). Specifically, the sequence data indicated that a contiguous region of 165,135 bp located at 4790733..4955867 in the reference sequence  had increased read coverage.
The Pst DC3000(H0457) isolate used to generate the reference sequence described by Buell et al., 2003 was re-sequenced using Illumina short read methods. A. Alignment of the observed reads to the reference sequence indicated higher than expected read coverage between genomic coordinates 4790733..4955867. This profile shows the absolute read depth coverage for the Pst DC3000 chromosome. Note that the origin of replication (ori) is on the left and right ends, and the terminus (ter) is in the center, close to position 3×106. Red and green lines show the number of reads matching the positive or negative strand of the chromosome, respectively. B. Copy number analysis indicated that read coverage was increased by two-fold above the expected average. For a complete list of all 1000 bp regions with altered read coverage, see Table S2. The ori-ter sequence content gradient is also visible, with more sequence coverage at regions closer to the ori as would be expected in growing cells with multiple rounds of replication proceeding concurrently. The region with anomalous coverage is oriented so that one end is closer to the ter. We refer to the ter-proximal end of the duplicated sequence as the left end and the ter-distal end as the right end.
Illumina sequencing results for the Pst DC3000(H0457) genome were analyzed to determine the degree to which the copy number had been altered in the 4.7 to 4.9 Mbp region. The fold coverage was determined for all 1,000 bp genome sequence blocks relative to an expected local average. The expected local average was computed across the genome to adjust for any differences in read depth due to the origin of replication-to-terminus (ori-ter) sequence content gradient (Fig. 1B). The average relative read depth for the entire genome was very close to the expected one-fold read coverage (mean = 1.01 stddev = 0.18). Regions with anomalous coverage were identified by scanning successive 1,000 bp blocks starting at the genomic origin in order to identify windows with relative read depth coverage that differed by more than three standard deviation from the expected local average (Fig. 1B and Table S2). The analysis showed that the portion of the genome between 4790733..4955867 had a read coverage very close to two-fold (mean = 1.94 stdev = 0.20) relative to the expected local average, consistent with duplication of the 165 kb region. Based on these results we refer to this region as the 165 kb duplication throughout the rest of the paper. We note that the data also suggest other genomic regions with less than the expected local average sequence coverage (0.58–0.62) relative fold read coverage, Table S2). We did not examine these regions further, but they may represent deletions within a portion of the sequenced cells or the results may be related to the non-uniform progress of DNA replication.
The 165 kb duplicated sequences are organized as a tandem duplication
The 165 kb duplicated sequence is flanked by 2059 bp ISPsy5 insertion sequence (IS) elements oriented as direct repeats relative to each other. The length of these repetitive elements makes it impossible to map the location and orientation of the second copy using only Illumina short read sequence data. Genomic duplications commonly form by unequal crossing over between two homologous IS elements at different locations  and are predicted to have a structure similar to that shown in Fig. 2A, with each duplicated segment bounded by repetitive DNA elements. PCR was used to test whether the 165 kb duplication in Pst DC3000 had this structure. A product of the predicted size was obtained using primers that anneal at each end of the 165 kb duplicated sequence, consistent with the head-to-tail configuration of a tandem duplication (Fig. 2A).
Each copy of the 165-to-black gradient. The duplicated sequences are flanked by ISPsy5 elements, which are depicted by two white triangles. A. PCR with oSWC4356 and oSWC4377 generate a 4041 bp product when using Pst DC3000(H0457) genomic DNA as template. No product is generated using the same primers when genomic DNA from a Pst DC3000 isolate lacking the duplication (see below) was used as template (-Cntl). B. The central ISPsy5 element was deleted and replaced with the kanamycin resistance encoding neo gene using recombineering. PCR with primers flanking this locus (oSWC4412 and oSWC4413) generate a 6630 bp product when the ISPsy5 element is present and a 2071 bp product in cells where the neo gene has replaced the central ISPsy5 element. PCR products were resolved on 1% agarose gel and migration in the predicted size range. M, indicates molecular weight marker.
The arrangement of the 165 kb duplication was also probed using recombineering (Fig. 2B). We reasoned that if the 165 kb duplication had the structure of a tandem duplication, then it should be possible to delete the central ISPsy5 using a recombineering substrate with homology to the 3′ and 5′ ends of each 165 kb copy. Pst DC3000 cells containing a recTEPsy expression plasmid were transformed with a 1305 bp PCR product containing the kanamycin resistance encoding neo gene and 80 and 85 bp of homology to regions flanking the central ISPsy5 element. PCR screening of several kanamycin resistant clones indicated that they (12/12) contained the specified neo insertion/deletion and two of these clones were further confirmed by sequencing the PCR product. The results show that the central junction was deleted and replaced with the 1.3 kb neo gene cassette in these clones exactly as predicted (representative result shown in Fig. 2B). These results confirm a tandem duplication structure, however, it does not address the possibility that the 165 kb region is present as a higher order repeat (i.e., triplication, etc.). In this scenario the deletion of a single junction would leave the other internal ISPsy5 junctions intact. To test this, we examined the kanamycin resistant clones to determine if any retained an internal junction. However, none of 12 recombinants tested generated this type of PCR product. Together, with the copy number analysis (above) these results support the conclusion that the 165 kb region is a tandem duplication and not a higher order amplification.
ISPsy5 is a member of the IS66 family, which generally produces 8 bp target site duplications . The sequences flanking the ISPsy5 elements were analyzed to determine the transposon-genome junctions and the direct repeats produced by the two annotated ISPsy5 insertions flanking the 165 kb duplication. Alignment of the sequences at the ends of the transposon suggests that the ISPsy5 elements have 22 bp imperfect terminal inverted repeats (Fig. S3) and produce 8 bp direct repeats upon insertion (Fig. 3). Production of an 8 bp target site duplication was verified by comparison of the left ISPsy5 locus of Pst DC3000 to that of its parent, Pst NCPPB1106, which does not have an ISPsy5 at this location or the duplication (see below).
A. Target site duplications associated with each ISPsy5 element in the 165(blue and green shading) for each ISPsy5 element (gray box, only 4 terminal base pairs are shown) in the 165 kb duplication were determined by Sanger sequencing PCR products that cover each loci.
When tandem duplications form by unequal crossing over between IS elements located at different sites on sister chromosomes they are predicted to generate a sequence configuration in which the target site duplication flanking the central element are derived from the two outer IS elements  (Fig. 3A). Sequence comparison of the 8 bp target site duplications flanking each ISPsy5 element associated with this tandem duplication confirmed that the central IS element is flanked by direct repeat sequences from the two outer elements, consistent with the duplication having formed by unequal crossing over (Fig. 3B).
Allelic variation at the 165 kb locus in sequenced Pst isolates and derivatives
Whole genome sequencing was used to determine whether the 165 kb duplication was present in other Pst isolates. In addition to Pst DC3000(H0457), nine other Pst genomes were sequenced (Table 1). Seven of these isolates were derived from the Pst DC3000(H0457) either by subculture (Table 1, Pst DC3000(ATCC, PS1, JB, BB, ZB, LS) or by genetic manipulation (Pst DC3000(D36E) is a Pst DC3000(H0457) derivative in which 36 confirmed effectors have been deleted). Pst DC3000(JF) is an independently propagated Pst DC3000 and Pst NCPPB1106 is the progenitor of Pst DC3000 , . Sequencing based copy number analysis indicated that the 165 kb duplication was present in five isolates. However, two isolates derived from Pst DC3000(H0457) by genetic manipulation (Pst DC3000(D36E) or by in vitro culture (Pst DC3000(JB)) did not have the 165 kb duplication (Fig. S4). Additionally, the independently propagated Pst DC3000(JF) and the progenitor of Pst DC3000(Pst NCPPB1106) did not show any evidence of the 165 kb duplication. PCR was used to test for the presence of the duplication in the sequenced isolates (Fig. 4). In all cases except for one the PCR results were consistent with sequencing based copy number analysis. The exception was Pst DC3000(JB), which PCR indicated (data not shown) it carried the Class I genotype similar to Pst DC3000(H0457) in Fig. 4. This discrepancy may be due to bona fide loss of the duplication in the sequenced clone and not in the stored freezer stock or possibly due to a technical limitation of the copy number analysis method.
Three primers (oSWC4416, oSWC4356 and oSWC4377) were used in PCRs with different Pst isolates as template. A. Multiplex reactions can distinguish three classes of genetic architecture at the 165 kb duplication locus. Class 1 has the full 165 kb tandem duplication; Class 2 does not have the duplication, but has the pair of ISPsy5 elements framing the 165 kb region; Class 3 does not have the duplication or the ISPsy5 on the left flank of the 165 kb region. B. PCRs resolved on 1% agarose gels show products representing the three varieties of alleles. The genomic DNA used as template in PCRs is shown above each lane. DC3000(Buell) indicates PCR using Pst DC3000 genomic DNA that was prepared for the genome sequencing reported in Buell et al., 2003 . All other strains are listed in Table 1. M, molecular weight marker. PCR using oSWC4416 and oSWC4377 occasionally generated minor 1 kb product, as seen in Pst DC3000(ATCC) and Pst DC3000(Buell). The band was extracted from the gel and sequenced. BLAST analysis indicated that the minor product corresponded to coordinates 4978742..4979422 in the Pst DC3000 genome sequence. This region is more than 22 kb downstream from the 165 kb duplicated region and most likely formed as a result of mis-priming.
All isolates containing the duplication were identical over the entire 165 kb region, suggesting that the duplication was recently acquired. However, we did find an interesting polymorphism among the isolates that lack the 165 kb duplication. First, the near-effectorless deletion derivative, Pst DC3000(D36E), appears to lack the duplication, but retains a copy of ISPsy5 at each end of the 165 kb locus (Fig. 4). In comparison, Pst DC3000(JF) and Pst NCPPB1106 lack both the duplication and the left end ISPsy5 element. These polymorphisms were confirmed by Sanger sequencing PCR products that covered the left ISPsy5 integration site. Together, these results suggest that in the course of laboratory propagation, Pst DC3000(H0457) acquired an ISPsy5 insertion at the left end of the 165 kb region (Pst DC3000 genome coordinate 4790732) and that this IS element provided the homology that led to duplication of the 165 kb region. Additionally, the discovery of this polymorphism also allowed us to confirm the eight base target duplication generated upon ISPsy5 insertion, as mentioned above.
PCR experiments used to confirm the presence of the duplication were also used to test a sample of genomic DNA (provided by Robin Buell, Michigan State University) that was left over from the original Pst DC3000 sequencing effort reported by Buell et al., 2003 . This PCR confirmed that the Pst DC3000 genomic DNA used to generate the reference sequence contained the 165 kb duplication (see DC3000(Buell) in Fig. 4B).
Duplication conditionally affects growth
Genomic duplications are part of the evolutionary toolbox and can dramatically change a cell's phenotype. The magnitude and direction of the change depends on the costs and benefits associated with the characteristics of a specific rearrangement. For example, doubling the copy number of genes can increase expression and provide a benefit; or negatively impact fitness through increased metabolic burden associated with additional sequence replication/maintenance or replichore imbalance .
To determine whether the 165 kb duplication affected the phenotype of Pst DC3000 cells, the majority (163,216 bp) of the left copy was deleted using recombineering to generate Pst DC3000(dup165−) (Fig. S5). The growth of the Pst DC3000(dup165−) deletion mutant was compared to Pst DC3000(H0457) in rich (KB) and minimal (MG) liquid growth media (Fig. 5A). Surprisingly, Pst DC3000 cells containing the duplication grew better than cells in which the duplication had been removed. The effect of the duplication on growth was most pronounced in rich medium, where duplication carrying cells grew approximately 44% faster in log phase (Fig. S1) and reached a higher final density before reaching the stationary phase. The improved growth of duplication containing cells was also detected in minimal medium, but only when the cells were in the log phase and growing at the fastest rate (Fig. 5A).
The growth of Pst DC3000 that contains the 165 kb duplication was compared to isogenic Pst DC3000(dup165-) cells with the duplication removed. A. Shows the phenotype of cells grown in rich (KB) and minimal (MG) media. B. 3×104 cfu/ml of Pst DC3000 or Pst DC3000(dup165-) were infiltrated into four-five week old tomato (Solanum lycopersicom ‘Moneymaker’) plants. The number of bacterial cells per square centimeter of leaf tissue was determined at two and five days post inoculation. Leafs show disease symptoms at five days post inoculation.
The 165 kb region contains 140 annotated protein coding genes. The functional roles  of each gene were reviewed to determine whether any might contribute to the growth phenotype or confer other important characteristics (Fig. 6 and Table S3). Overall, the range of functions encoded within the 165 kb region did not differ substantially from the genome-wide statistics (Fig. S6). Nevertheless, the annotation suggested that four genes within the 165 kb region had functions associated with pathogenesis; these are gor-2, pnlA, sodB and hopE1 (Table S3). We tested whether the duplication influenced the ability of Pst DC3000 to function as a virulent pathogen on tomato. Plants were infiltrated with Pst DC3000(H547) or Pst DC3000(dup165−); symptoms were observed over 5 days and the growth of the bacteria was assessed on days two and five post inoculation. No significant differences in disease or in planta growth were noted (Fig. 5B), suggesting that the growth defect observed in vitro does not affect the bacterial physiology with respect to its pathogenic lifestyle.
The functional roles for the 140 genes in the 165-Comprehensive Microbial Resource (JCVI-CMR) Cellular Role Category annotation . The JCVI-CMR Cellular Role Category annotation for each gene in the duplication is shown in Table S2.
Dynamic properties of the 165 kb duplication in Pst DC3000
As noted above, we observed that the 165 kb duplication was absent in some Pst DC3000(H0457) derivatives i.e., see Pst DC3000(D36E) in Fig. 4. Since these types of duplications are known to be unstable , it would not be surprising if some other Pst DC3000 mutants differ with respect to the presence of the duplication. Consistent with this idea, we observed the growth phenotype of a Pst DC3000 mutant change after a routine genetic manipulation using allelic exchange mutagenesis to delete a gene. In this case, the iaaL gene was deleted from Pst DC3000(D28E). The deletion strain consistently yielded larger colonies than the Pst DC3000(D28E) parent on KB agar plates (Fig. 7A). The difference in growth was confirmed using a growth curve in liquid KB broth (Fig. 7B). Furthermore, expression of the iaaL gene in trans failed to complement this phenotype (Fig. 7C), suggesting that absence of iaaL was not responsible for the altered growth. PCR confirmed that Pst DC3000(D28E) and the iaaL mutant strains differ in their duplication status (Fig. 7D). Because the constructed duplication deletion mutant, Pst DC3000(dup165−) (Fig. 5 and Fig. 7) also exhibits slow growth phenotype in rich medium, this finding provides a second example linking the growth phenotype with the duplication and raises the possibility that there is positive selection for the duplication in cells growing under laboratory conditions.
A spontaneous mutant that had reformed the 165°C. B. The Pst DC3000(D28E ΔiaaL) mutant had an increased growth rate in rich (KB) broth medium. C. Expression of the iaaL gene in trans does not complement growth phenotype of the Pst DC3000(D28EΔiaaL) mutant. D. The duplication was present in Pst DC3000(D28EΔiaaL), but not in the parental Pst DC3000(D28E) strain. PCR with primers oSWC4356 and oSWC4377 produce a 4041 bp product when the duplication is present. No product is formed when the duplication is absent. Lane marked ‘M’ indicates molecular weight marker.
Genomes are the fundamental structural and operational unit of life, upon which all genetic and regulatory information are organized, utilized and stored. Genomes also have adaptive functions that allow evolution to proceed by the capacity to balance stability with change. The pace and targets of change are influenced by genomic organization, suggesting that the flexibility we observe is the product of many successful evolutionary steps. In bacteria, genome fluidity is mechanistically linked to horizontal gene transfer, mutation and intrachromosomal recombination. Here we describe an example of genome fluidity mediated by the latter and show that IS elements can contribute to this process by serving as segments of mobile homology that can facilitate recombination. IS-mediated duplications are a useful evolutionary device because they occur readily, usually do not cause loss of function, and can collapse back to single copy if a selective advantage is not produced; an evolutionary gamble with very low stakes. In the long term, duplications serve as the birthplace for novel functions by providing additional sequences that can accumulate mutations and allow diversification without compromising essential activities .
Identifying the 165 Kb duplication in Pst DC3000
The Pst DC3000 genome sequence was reported in 2003  and was later resequenced as a proof of concept for genome assembly using short read sequence data . It is not surprising that neither report described the presence of the 165 kb duplication, because the ISPsy5 insertion sequence elements that flank the region complicate identification and mapping strategies. IS elements and other repetitive sequences, that are too long to be spanned by a continuous sequence read, make tandem duplications impossible to directly map. In general, short read sequences derived from any repetitive DNA element that cannot be spanned by a single read are considered “unmappable” and their location must be inferred by the unique sequence joints at the 5′ and 3′ ends of the repetitive element. We detected the presence of the duplication in Illumina short read sequencing using profiles showing read coverage for the entire genome; similar observations were described in Salmonella . To quantify the change in copy number, we developed a computational strategy that compensated for the ori-ter replication gradient. This approach implements ideas presented by Skogaard et al., 2011  and should have utility for identifying other large-scale changes that alter genome structure.
The copy number analysis indicated that a 165 kb region had doubled. The structure of the duplication was probed using PCR and recombineering, and further verified with traditional Sanger sequencing. The duplicated region accounts for 2.6% of the total genome and contains 140 annotated protein-coding genes, including the hopE1 virulence effector gene , . The duplication is flanked by 2059 bp ISPsy5 elements. We note that there are 33 complete copies of the ISPsy5 element in the Pst DC3000 reference sequence which could facilitate other genomic rearrangements.
The 165 kb duplication formed in domesticated Pst DC3000 isolates
The Pst DC3000 strain became a model bacterium largely because of pioneering work that demonstrated this strain was capable of DNA uptake (transformation and conjugation)  and could cause disease on Arabidopsis . The Pst DC3000 strain was isolated in the mid-1980's as a spontaneous rifampicin resistant mutant of Pst NCPPB1106, a feature that was used to select for conjugal recipient clones , . It was at this point, that the evolutionary trajectories of the two strains diverged. We analyzed Pst NCPPB1106 for the presence of the 165 kb duplication to determine if it had been present before Pst DC3000 was isolated and therefore likely to be propagated to all Pst DC3000 strains and derivatives. We found that Pst NCPPB1106 did not have the duplication or the ISPsy5 insertion and target site duplication that marks the left boundary of the duplicated region. Because the IS elements likely provide the necessary homologies for formation of the tandem duplication, the lack of the ISPsy5 insertion at this location is strong evidence that Pst NCPPB1106 has never had the 165 kb duplication. It also implies that not all Pst DC3000 isolates necessarily contain the duplication or the homology needed for it to form. Consistent with this hypothesis a Pst DC3000 isolate obtained in 2012 from Jacqueline Fletcher at Oklahoma State University contains the Pst NCPPB1106 allele (see Pst DC3000(JF) in Fig. 4) confirming that at least one Pst DC3000 isolate did not inherit the duplication.
The absence of the left end ISPsy5 in Pst NCPPB1106 suggests that the 165 kb duplication in Pst DC3000 likely formed in two steps since these strains diverged. First, an ISPsy5 element inserted at Pst DC3000 genome coordinate 4790732, which forms the left boundary of the affected region and introduced the homology necessary for the next step. Second, a recombination event occurred between the IS elements at the left and right boundaries, likely by an unequal crossing over, that resulted in formation of the tandem duplication.
The duplication confers a selective advantage in some conditions
Given our current understanding of the relationship between genes, copy number and genomic organization, it is very difficult to predict whether a duplication will have phenotypic effects, especially in terms of any emergent characteristics that might arise from the interplay between these features. Even so, duplications can alter the phenotype of cells that contain these structures (for review see , ). We found that the 165 kb duplication affected the phenotype of Pst DC3000 in conditions that support rapid growth. Under these conditions, the duplication-containing Pst DC3000(H0457) strain grew more vigorously and to a higher final density compared to the mutant lacking the duplication (Fig. 5A).
It is important to note that we did not detect any difference in disease or in planta growth associated with the 165 kb duplication (Fig. 5B), suggesting that any variability in the duplication status is unlikely to effect analysis of P. syringae virulence systems. Additionally, this result provides information about Pst DC3000 in planta growth dynamics. Because we did not see any difference in in planta growth between cells that differed in duplication status, this supports the idea that the apoplastic environment is more similar to minimal media than rich broth conditions , and that cells grow relatively slowly in planta compared to in rich broth.
In general, finding a persistent duplication can be taken as evidence of positive selection. Based on our phenotypic observation, it's likely that the duplication has become fixed in some Pst DC3000 strains because of the fitness advantage these cells possess in rich culture. We do not yet have a mechanistic explanation for how the duplication enables faster growth. We found no evidence of SNPs between the duplicated copies in the whole genome sequence data, suggesting that the duplication was recently acquired and that any observed phenotypic affects were unlikely a result of gene-level functional adaptation. Therefore, it seems that the growth phenotype is either a result of increased copy number or altered genomic organization. Gene copy number amplification has been proposed to explain the now classic (and provocative) results of Cairns and Foster , who found lac− revertants able to grow on lactose at a frequency higher than could be explained by the normal mutation rate. The amplification mutagenesis model holds that duplication and higher order gene amplification can enable cells to survive nonpermissive growth conditions by providing additional copies of genes that are weakly beneficial in that environment . Similar biological phenomena are likely in operation with the 165 kb duplication. There are 140 genes encoded in this duplicated region and it is possible that increased expression of one or more of them enables cells to grow better than single copy peers in rich media conditions.
Flexibility and stability
It did not escape our attention that the altered in vitro growth characteristics of the duplication deletion Pst DC3000(dup165−) were similar to the growth phenotype of the near-effectorless Pst DC3000(D36E) mutant. The growth phenotype noted in the Pst DC3000(D36E) strain arose spontaneously in several independent mutant lines generated in the course of producing the near-effectorless mutants, i.e., Pst DC3000(D28E) . The altered growth phenotype of the effector polymutant strains was initially observed as colonies that were markedly smaller when plated on KB (rich) agar medium (Fig. 7A) and grew to the same size as wild type on minimal (MG) agar growth medium . This led us to hypothesize that the growth defect of the Pst DC3000 multiple effector mutant strains was attributed to the status of the duplication. This hypothesis was supported by two observations. First, Pst DC3000(D36E) and an earlier deletion derivative Pst DC3000(D28E) (in which the 28 most highly expressed effectors have been deleted) lacked the duplication and did not grow as well in rich medium as strains containing the 165 kb duplication (Fig. 7). Second, in the course of a routine genetic manipulation (deletion of iaaL from Pst DC3000(D28E), see material and methods) we observed a spontaneous reversion to the enhanced growth phenotype (Fig. 7) and when we assayed for the presence of the duplication using PCR we found that the duplication had returned (Fig. 7D). Expression of the deleted iaaL gene from a plasmid did not complement, supporting the notion that it is not responsible for the growth phenotype (Fig. 7C). The identification of strains in which the 165 kb duplication spontaneously fluctuates demonstrates the dynamic nature of these sorts of genomic rearrangements and provides further evidence implicating the duplication with the growth phenotype.
Tandem duplications are notoriously unstable. Formation, loss and amplification of this type of duplication are predicted to occur at high frequency . In Salmonella typhimurium, the frequency of duplication at most genomic loci is between 10−3 and 10−4 . There is also a high rate of loss, which led to the proposal that the observed presence of duplications in a population represents a steady state. In an unselected population, its estimated that approximately 1 cell in 1000 contains a duplication . This implies that the Pst DC3000 genome experiences a certain degree of flux and that what we observe (either physically or phenotypically, i.e., via sequencing or genetics) represents a steady-state equilibrium of the analyzed population.
Relevance to P. syringae biology
Speculation regarding the role of IS elements in promoting recombination in P. syringae began shortly after repetitive sequences were found in association with the first avirulence gene cloned from these bacteria . Since then, many examples of P. syringae virulence genes located near or in association with mobile genetic elements have been found and the idea that these elements might facilitate recombination has been a recurring theme , , . Moreover, comparison to diverse P. syringae strains suggests that members of the Pst DC3000 phylogenetic clade have evolved to use transposons to generate diversity more than other P. syringae groups , . It is striking that 5% of Pst DC3000 ORFs are annotated as having functions related to transposition . Additionally, there is evidence of recent transposon activity in Pst DC3000 that altered genomic content of some laboratory isolates . These characteristics and the results described here suggest the Pst DC3000 genome has some structural fluctuation, which in some cases may provide advantages in certain environments.
Analysis of growth rate data for Pst DC3000 and Pst DC3000 (dup165−) grown in KB medium. Main plot: Approximate instantaneous growth rates for each strain, calculated by numerically differentiating the log-transformed growth curves log2(N/N0) vs t. Growth rates are reported as an inverse doubling time (hr−1). Inset plot: Estimated ratio of Pst DC3000 to Pst DC3000(dup165−) growth rates, using both the unsmoothed data shown in the main plot (black), and smoothed versions of the growth rate data (red), doing the smoothing with a boxcar filter of width 10. From the inset, it can be seen that during the first 6 hours, Pst DC3000 grows at a rate approximately 44% times faster than Pst DC3000(dup165−).
ChIP-seq experiments revealed the presence of genomic rearrangements. Illumina sequencing results shown are from control samples used in ChIP-seq experiments to identify iron starvation sigma factor binding locations. The number of sequence reads (Y-axis) for each position of the genome (X-axis) is shown as a histogram. These results indicate that the region spanning 4790778..4955784 in the annotated Pst DC3000 sequence had approximately twice the local average number of sequence reads. The data shown here were described as negative controls in ChIP-seq experiments analyzing the regulons iron starvation (IS) sigma factors , . In these IS sigma factor studies, enrichment and non-specific immunoprecipitation were evaluated by comparing the number of sequence reads at each locus in experimental samples versus reads from controls prepared from Pst DC3000 cells containing the empty vector (pBS60). This control was treated identically to cells expressing the epitope tagged sigma factor , . The duplicated DNA sequence is visible as doubled DNA content near 5e+06 bp. The partition of the Pst DC3000 replichores was also suggested in the ChIP-seq results. For example, we observed that genomic DNA proximal to the presumed origin of replication was more abundant relative to parts of the chromosome where replication is expected to terminate. This is likely due to the presence of multiple replication forks proceeding bidirectionally from the origin of replication , . Red and green histograms show the number of sequence reads matching the positive and negative strands of the Pst DC3000 genome sequence , respectively.
ISPsy5 inverted repeats. Boundaries of the ISPsy5 elements were identified by searching the Pst DC3000 genome sequence using Blast with a representative ISPsy5-containing sequence as the query. The 5′ ends of each end were aligned and internal boundary of the inverted repeats was determined as the point where the sequence identity between the two inverted repeats fell below 80% using a 10 bp sliding window.
Copy number analysis of Pst genome sequences. Whole genome assisted copy number analysis was used to determine whether genome sequences show evidence of genomic duplication. Pst DC3000(JF) does not have the 165 kb duplication, but shows evidence of another genomic expansion at 5369001..5402000, which is also flanked by ISPsy5 elements.
The left hand (terminus proximal) copy of the duplication was deleted. The genome coordinates of this deletion are 4790396..4953611. Recombineering was used to delete 163,216 bp of the left copy of the duplication and replaced with the kanamycin resistance encoding neo gene. PCR and sequencing were used to confirm deletion of the duplication. PCR products were resolved on a 1% agarose gel. M, molecular weight marker.
Functional roles of genes within the duplication do not differ substantially from the genome-wide proportions. The functional role categories for the Pst DC3000 genome were obtained from JCVI Comprehensive Microbial Resource database . The fractional representations of genes from each category are shown for the entire genome (all) in blue and for the 165 kb duplication (dup) in green.
Areas of the Pst DC3000(ATCC) genome with altered copy number. Illumina sequencing results for Pst DC3000(ATCC) genome were analyzed to identify genomic regions with anomalous read depth coverage. The relative read depth of 1,000 bp genome sequence blocks was determined in relation to the expected local average. The expected local average was computed across the genome in order to adjust for differences in read depth due to the replication-to-terminus sequence content gradient. The average relative read depth coverage for the entire genome was approximately one (log2 mean = −0.02 stddev = 0.23). Windows of 1,000 bp with relative read depth coverage that differed by more than three standard deviation from the local average are shown above. Relative sequence read depth is a log2-transformed measure of read depth (X), retransformed back to the linear space (2X) to produce the Estimated copy number. Regions with doubled relative sequence coverage do not map exactly with the predicted duplicated region because the resolution of this copy number analysis is lower due to the requirement that the entire 1000 bp region have an average that is more than three standard deviations from the expected local average and because each end of the duplicated region terminates with unmappable ISPsy5 elements.
Genes and functional role categories contained within the 165 kb duplication. Multiple JCVI categories are separated by a “/”. In instances where a gene does not have a JCVI category assigned, the primary genbank annotation is shown. Genes annotated as having roles in pathogenesis are indicated with “♦”. Genes in the same functional role category are indicated by the color of background shading. *Disrupted reading frame. ** No JCVI Cellular role category information.
We thank Diane Cuppels for Pst NCPPB1106, Robin Buell for the genomic DNA used in the original Pst DC3000 sequencing, Jacqueline Fletcher for Pst DC3000(JF), Kent Loeffler for photography, Bronwyn Butcher and Qiaojuan Shi for technical support with Illumina sequencing and Mick Chandler for advice on identifying inverted repeat sequences and for suggesting that the arrangement of the target site duplications could provide evidence of the mechanism of duplication. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. The USDA is an equal opportunity provider and employer.
Conceived and designed the experiments: ZB PVS CRM HL SWC BS SC. Performed the experiments: ZB HL PS. Analyzed the data: BHK SWC PVS CRM AC BS. Contributed reagents/materials/analysis tools: AC HL PS SWC HL HLW SC BHK. Wrote the paper: BS CRM PS ZB.
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