Ecologically Significant Genetic Loci of <i>P. allii</i> : Contributions to Pathogenesis and Competition
Bibliographic record
Abstract
Abstract Pantoea allii , one of four Pantoea species known to cause onion center rot, is infrequently isolated from onion compared to its closely related onion-pathogenic sister taxa. To better understand the genomic diversity and genetic determinants of pathogenicity in this species, we analyzed a collection of 38 P. allii strains isolated from two primary ecological niches, plants and water, across three continents using comparative genomics and phylogenetic approaches. Core-genome phylogeny, average nucleotide identity (ANI), and gene presence–absence analyses revealed three genetically distinct lineages. All strains harbored conserved biosynthetic gene clusters (BGCs) for quorum sensing, carotenoid production, siderophores, and thiopeptides. In contrast, two phosphonate BGCs, key determinants of onion pathogenicity, exhibited lineage-specific distributions. Onion-associated strains from Lineages 1 and 2 carried the Halophos BGC associated with onion tissue necrosis, and onion isolates encoded the alt gene cluster conferring thiosulfinate tolerance. Lineage 3 strains, isolated from both onion and rainwater, either lacked a phosphonate BGC loci or carried the HiVir phosphonate BGC. In addition, Lineage 3 strains lacked the alt cluster altogether. The localization of these virulence genes in the genome varied, with Halophos integrated in the chromosome, HiVir encoded on the conserved Large Pantoea Plasmid, and alt located on a small, variable plasmids (plasmid B). The Type IV and Type VI secretion systems showed variable genomic architectures, with plasmid-borne T4SSs and two chromosomal T6SS loci differing in conservation and gene content. Additionally, conserved Pantailocin phage islands were detected in most genomes. Overall, this study reveals that while core metabolic and competitive traits are conserved across P. allii , virulence-associated loci display lineage-specific partitioning, reflecting ecological differentiation and evolutionary plasticity within the species. Impact Statement This study presents a comprehensive comparative genomic analysis of available Pantoea allii genomes, a known onion pathogen. By analyzing 38 strains isolated from plant and water sources across three continents, we uncovered lineage-specific distributions of key virulence genes, alongside conserved genetic traits associated with competition and environmental resilience. These findings clarify the genetic basis of P. allii pathogenesis and highlight its potential as a biocontrol agent, offering broader insights into how ecologically significant loci contribute to the dual roles of plant-associated bacteria as both pathogens and beneficial microbes. Data Summary PENDING
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".