The Pseudomonas syringae complex is a phylogenetic group comprising at least fifteen bacterial species and more than sixty host-specialized pathovars that collectively cause disease in over 180 plant species, including virtually all economically relevant crops. In highbush blueberry (Vaccinium corymbosum), infections manifest as blight of leafy tissues or cankers of woody tissues, both of which reduce plant health and productivity. Disease development depends on the transition of the bacterium from an epiphytic phase, in which cells remain adhered to plant surfaces, to an endophytic phase involving colonization of internal structures and the release of tissue-destroying virulence factors. Environmental conditions common in British Columbia—cool temperatures, high humidity and frequent precipitation—favour the growth and motility of epiphytic populations and thereby increase the likelihood of endophytic infection, making strategies that reduce surface populations before infection establishes an attractive line of defence.

The economic stakes are considerable. Global blueberry production reached roughly 2.14 billion kilograms in 2024, and Canada is the fourth-largest producer worldwide, accounting for nearly one-sixth of global output. Canadian blueberry exports were valued at approximately CAD $695 million in 2024, representing more than 65 percent of all Canadian fruit exports. Nearly 94 percent of the country’s highbush blueberry production occurs in British Columbia, where conditions favourable to the crop simultaneously favour bacterial growth and dispersal on plant surfaces. Traditional management has relied on copper-based biocides, but this approach damages the natural environment, can stunt plant growth through interference with the rhizosphere microbiome, and has been losing efficacy due to the spread of plasmid-borne copper resistance genes. Mitigation is often limited to the costly and unsustainable practice of pruning or culling infected plants.

Against this backdrop, the research team isolated bacteriophages from wastewater samples and from Pseudomonas syringae complex-infected blueberry plants collected at sites in the lower mainland and Okanagan valley regions, ultimately obtaining nineteen relatively stable phage isolates. Because phage predation by individual phage species is generally restricted to a subset of target strains and readily selects for resistant subpopulations, cocktail formulations of multiple distinct phages are typically employed to expand host range, improve efficacy and forestall resistance. The researchers used a semiquantitative spotting analysis to score infection interactions between each phage and a panel of twenty bacterial strains on a scale from zero to four, then excluded seven isolates—deemed weak specialists—that fell below median thresholds for both the number and strength of interactions. Twelve candidate phages advanced to genomic and functional characterization.

Whole-genome sequencing revealed extensive phylogenomic diversity among the candidates. Three isolates proved to be variants of a species within the genus Unosvirus, three were clonal duplicates belonging to Pifdecavirus, and a further group of four—three clonal and one diverged—may represent a novel species within an as-yet-undefined genus most closely related to Pseudomonas phage QdP_Psa3. The most striking discovery was phage φCB10, a jumbo phage with a genome of approximately 310 kilobases encoding 476 predicted coding sequences, most of them of unknown function. φCB10 was unrelated to the other lineages, most closely resembled Pseudomonas jumbo phage Psa21 at only 53.2 percent genomic similarity, and may represent the founding member of a novel genus. All twelve candidates were predicted to be obligately lytic, and bioinformatic screening found no lysogeny-associated genes, antimicrobial resistance determinants or metal resistance cassettes—characteristics considered indispensable for safe agricultural biocontrol.

Environmental stability assays revealed considerable heterogeneity among isolates. Exposure to ultraviolet radiation for one hour reduced viable titres of all phages, with the severity depending on wavelength: under UV-A at 365 nanometres, relevant to field conditions, only φCB16 fell below the detection limit, whereas UV-C at 254 nanometres drove the titres of most phages below detection. Freezing at −20 degrees Celsius produced a particularly polarizing split along predicted morphology: the three myovirus-like phages lost roughly 1.6 to 3.4 orders of magnitude in titre within a single day and became undetectable after 30 days, while podovirus-like isolates fared substantially better, with φCB02 and φCB05 showing no significant losses over the full month. This partitioning suggests that virion structural properties may broadly influence environmental persistence, a phenomenon the authors say warrants mechanistic investigation. Notably, some isolates appeared more stable at 22 degrees Celsius than at the conventional 4 degrees Celsius storage temperature, raising questions about the universality of phage storage conventions. Prolonged exposure to highly acidic conditions, potentially relevant given that blueberries thrive in soil at pH 4.0 to 5.5, was among the most consistently destabilizing stresses, although most phages retained functionality over biologically relevant timescales.

To quantify antibacterial activity, the team performed planktonic killing assays against eight virulent bacterial strains, summarizing 64 phage-host pairs with a Growth Reduction Coefficient derived from bacterial growth curves. Individual phage performance varied widely and depended strongly on the strain: the jumbo phage φCB10 achieved the highest median coefficient, 0.943, and was the only phage rated as strong across all targeted hosts, while roughly half of all single-phage interactions were deemed poor. The two most effective phages were variously combined with the four least effective to construct eight cocktails of three to five variants. Although cocktails did not significantly outperform individual phages overall, four formulations—φC_A, φC_B, φC_C and φC_D—achieved median coefficients above 0.75 and were rated as strong across the full host panel, and were carried forward to plant-based testing.

The decisive validation used a detached-leaf model in which young Draper-variety leaves were pretreated with phage cocktails and then inoculated with two highly virulent strains. Bacterial densities were substantially reduced in all pretreated leaves. At early timepoints corresponding to maximal bacterial densities in untreated leaves, the four cocktails induced reductions of 4.5 to 5.5 logs against strain B11 and 3.2 to 5.6 logs against strain B04. At the ten-day endpoint, two cocktails pushed B11 below the detection limit, and two others reduced B04 below detection. A variant of the Growth Reduction Coefficient calculated from bacterial density over time rated all four cocktails as strong against B11, with φC_D also strong against B04. Critically, ex planta performance correlated strongly with in vitro performance, suggesting that planktonic killing assays can serve as a useful proxy for more complex validation models in high-throughput screens.

Measurements of phage densities inside the leaves supported the conclusion that bacterial suppression was driven by ongoing lytic replication rather than a single contact-mediated kill. The mean in situ phage-to-bacterium ratio rose rapidly to a peak of roughly 1.8 × 10⁴ for treatments targeting B11 before decaying by day ten, and endpoint phage-to-bacterium ratios correlated positively with overall treatment efficacy. The authors interpret this as evidence that successful biocontrol depends not only on the killing efficiency of individual phages but also on their capacity to persist within the plant environment and maintain productive infections over extended periods.

The study establishes a framework for the systematic identification and evaluation of candidate phages for agricultural biocontrol, while flagging the questions that remain before field deployment. Detached-leaf assays cannot fully recapitulate whole-plant systems, and the authors emphasize the need to reproduce these results in larger-scale studies with intact plants and, ultimately, under field conditions, alongside assessments of any impacts on plant health or the native phyllosphere microbiome. The mechanisms governing phage susceptibility among bacterial strains also remain poorly understood. Meanwhile, φCB10—with its exceptional antibacterial performance, favourable stability, enormous coding capacity and potential to carry accessory functions capable of circumventing bacterial defence systems such as restriction-modification and CRISPR-Cas—stands out as a particularly compelling subject for future investigation, both as a biocontrol candidate and as a window into the biology of underexplored jumbo phages.

Subject of Research: Isolation and evaluation of bacteriophages for biocontrol of Pseudomonas syringae complex populations on highbush blueberry leaves

Article Title: Bacteriophages Control Epiphytic Pseudomonas syringae Populations in Highbush Blueberry Leaves

Article References: Ball, C., Lauman, P., Xu, T., Guy, T., Dadej, K., Richter, R., Lubberts, M., Cross, K., Ren, M., Latchman, S. R., Burlakoti, R., Deng, X., Fong, K., & Wang, S. (2026). Bacteriophages Control Epiphytic Pseudomonas syringae Populations in Highbush Blueberry Leaves. Microbial Biotechnology, 19(9), Article e70438. https://doi.org/10.1111/1751-7915.70438

Image Credits: AI Generated

DOI: 10.1111/1751-7915.70438

Keywords: bacteriophages, phage biocontrol, Pseudomonas syringae complex, highbush blueberry, Vaccinium corymbosum, plant pathology, epiphytic bacteria, jumbo phage, phage cocktails, agricultural biotechnology, British Columbia, leaf blight

Researchers Bin Li, Zhuqing Zheng and Ruiyi Fan of Jingchu University of Technology in Jingmen, China, constructed a UGT pan-genome spanning 23 cultivars of highbush blueberry, Vaccinium corymbosum. Their analysis identified a striking total of 11,696 VcUGT genes distributed across 662 orthologous gene groups, or OGGs. This substantially extends the previously cataloged inventory of 361 VcUGT members, which had been derived from the single ‘Draper’ reference genome. The finding underscores a lesson that is rapidly becoming a central theme of modern plant genomics: a single reference assembly, however high quality, captures only a fraction of the functional gene diversity present within a crop species, particularly one with a complicated polyploid genome like the autotetraploid highbush blueberry.

The structure of the pan-genome itself proved revealing. The researchers found it to be highly open, meaning that each additional cultivar sequenced continues to contribute new gene variants rather than quickly saturating the inventory. At the heart of the pan-genome sits a compact core of just 106 orthogroups, which nevertheless accounts for 57.5 percent of all gene copies, reflecting how frequently these conserved UGT lineages are duplicated within individual genomes. Surrounding that core is a remarkably plastic dispensable fraction of 556 orthogroups, including 374 so-called cloud orthogroups that are present in only a minority of cultivars. Notably, 328 of these cloud groups were cultivar-specific, meaning they exist in just one variety among the 23 examined, a level of divergence that hints at extensive gene birth, loss and reshaping during the recent history of blueberry breeding.

One of the most striking evolutionary patterns emerged when the blueberry UGT families were compared with those of Arabidopsis thaliana, the standard reference plant for genomic comparisons. Subfamily G, corresponding to the UGT85 lineage, showed an 18-fold expansion relative to Arabidopsis. Because highbush blueberry is an autotetraploid, carrying four copies of each ancestral chromosome set, the expansion translates to roughly 4.5-fold on a per-haploid-genome basis, still a dramatic proliferation. At the same time, clades involved in sterol metabolism and stress responses underwent reciprocal contraction, suggesting that during the evolutionary history of the Vaccinium lineage, the enzyme family was sculpted in a direction that favors the glycosylation of flavonoid-type compounds, the very chemistry that gives blueberries their characteristic pigments and antioxidant-rich composition.

To probe the selective forces acting on these genes, the team performed pairwise analyses of nonsynonymous to synonymous substitution rates, the classic Ka/Ks test, and examined the PSPG box, a highly conserved motif within the plant secondary product glycosyltransferase domain that plays a crucial role in recognizing the sugar donor substrate. The results indicated pervasive purifying selection acting on the catalytic core of these enzymes, consistent with the idea that the fundamental chemistry of sugar transfer is too essential to tolerate much tinkering. Natural selection appears to preserve the enzymatic machinery while allowing variation to accumulate in the regulatory and copy-number dimensions of the family.

That interpretation gained further support from the analysis of structural variants. Structural variants, encompassing insertions, deletions and inversions of substantial DNA segments, are increasingly recognized as major drivers of crop trait diversity, and the blueberry UGT pan-genome proved no exception. Pangenes affected by structural variants showed elevated paralog divergence specifically within the dispensable fraction of the genome, a pattern the authors interpret as consistent with relaxed rather than diversifying selection. In other words, freed from the strong functional constraints that govern the core gene set, dispensable UGT copies accumulated mutations and diverged from one another, generating raw material on which future selection, whether natural or breeder-directed, could potentially act.

In a display of methodological caution that stands out in an era of genome-scale enthusiasm, the researchers identified two extreme-length gene models belonging to the SNAP category and classified them as suspect or fused candidates. Rather than attempting to draw mechanistic conclusions from these anomalous models, they excluded them from functional interpretation pending transcript-level validation. This restraint matters because spurious gene predictions, particularly in complex polyploid assemblies where duplicated haplotypes can be misassembled into fused models, can mislead downstream analyses and breeders alike. By flagging and setting aside such cases, the study models a rigorous standard for pan-genome research in polyploid crops.

The comparative dimension of the work also delivered practical insights for breeding programs. Northern highbush and southern highbush blueberries represent two major cultivated groups, distinguished historically by their adaptation to cold-winter and mild-winter climates respectively, with southern highbush varieties developed by incorporating native Vaccinium species adapted to warmer conditions. When the researchers compared the two groups, they identified 15 orthogroups with significant group-biased presence between northern and southern highbush cultivars, and all 15 were confined to the dispensable fraction of the pan-genome. This pattern suggests that the genetic distinctions underlying cultivar-group differentiation include dispensable, structurally variable UGT loci, raising the intriguing possibility that variation in these glycosylation genes contributes to group-specific fruit quality characteristics or stress adaptation traits.

For breeders, the implications are direct and tangible. Anthocyanin and flavonol glycosylation influences the intensity and stability of fruit color, the accumulation of health-associated polyphenols, and potentially the shelf life and processing quality of berries, all of which are commercial priorities. The pan-genome catalog produced by this study provides a roster of SV-associated and dispensable UGT loci that now constitute candidate targets for functional validation and marker-assisted breeding. Rather than relying on a single reference genotype, breeders seeking to modulate polyphenol profiles or fruit pigmentation can consult a diversity-aware inventory that reflects the actual breadth of cultivated germplasm. As genomic selection and precision breeding techniques advance in horticultural crops, having an accurate map of which enzyme-coding families vary across varieties and which are anchored in the conserved core becomes a powerful navigational tool.

More broadly, the study adds blueberry to the growing list of crops, ranging from wheat and maize to tomato and potato, for which pan-genome analyses have exposed the limitations of reference-centric genomics. In polyploid species especially, where multiple haplotypes coexist within every individual, structural variation and presence-absence variation can hide entire gene families from view. The 11,696 VcUGT genes identified across just 23 cultivars, compared with the 361 cataloged from the ‘Draper’ reference, represent a more than thirtyfold difference in copy count, a vivid illustration of how much biology remains concealed within unsequenced diversity. As sequencing costs continue to fall and pan-genome frameworks mature, the blueberry UGT catalog will likely serve as a template for exploring other metabolically important gene families in Vaccinium and related ericaceous crops, connecting genome-scale discovery to the sensory and nutritional qualities that consumers experience with every handful of berries.

Subject of Research: Pan-genomic analysis of UDP-glycosyltransferase gene diversity and structural variation across highbush blueberry cultivars

Article Title: Structural variation and pan-genome dynamics shape the UDP-glycosyltransferase repertoire in highbush blueberry

Article References: Li, B., Zheng, Z., & Fan, R. (2026). Structural variation and pan-genome dynamics shape the UDP-glycosyltransferase repertoire in highbush blueberry. BMC Genomics. https://doi.org/10.1186/s12864-026-13376-5

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13376-5

Keywords: Vaccinium corymbosum, UDP-glycosyltransferase, pan-genome, structural variation, highbush blueberry, anthocyanins, flavonoid glycosylation, orthogroups, polyploid genome, marker-assisted breeding, gene family expansion, presence-absence variation