Complete Genome Sequence Resources for <i>Pseudomonas syringae</i> Strains 508 and TLP2
Bibliographic record
Abstract
Some naturally occurring isolates of the ubiquitous phytopathogen Pseudomonas syringae have been reported to be nonpathogenic despite sharing common pathology-associated genetic features. Here, we present the complete genome of two putatively nonphytopathogenic Pseudomonas strains, P. syringae strain 508 and P. syringae TLP2, which are members of Phylogroup 2c within the P. syringae species complex. Comparison with the closely related reference strain P. syringae pv. syringae B728a reveals at least two major structural rearrangements that are likely involved in bacteria–bacteria or bacteria–host interactions. One key rearrangement is the relocation of the pathogenicity island encoding the atypical variant of the type III secretion system (T3SS) to a location more than 270 kbp downstream, decoupling the genomic island from many genes in both the canonical conserved and exchangeable effector loci. This change coincides with a reduction of effector genes within the T3SS pathogenicity island and, more generally, a reduction of effector genes in the genomes of both nonphytopathogenic strains. Identification of regions of genetic mobility and novel targets using complete positional data will aid in the study of the genetic associations with phenotypic variability in phytopathology in P. syringae strains. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.006 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.020 | 0.024 |
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".