Pan-genome analysis of Ralstonia pseudosolanacearum associated with tobacco bacterial wilt in China
Bibliographic record
Abstract
Tobacco bacterial wilt, caused by Ralstonia solanacearum species complex (RSSC), poses a significant threat to tobacco production in most major tobacco-growing regions of China. Here, 204 strains of Ralstonia were isolated from infected tobacco plants across 12 provinces and autonomous regions in China. Molecular identification and biovar typing of the RSSC strains revealed that all the isolates were found in phylotype I (classified as R. pseudosolanacearum) and biovar III. Seven sequevars were identified and sequevar 15 was the most prevalent. Pathogenicity tests indicated that 29% of the strains showing high virulence were found in the southwest tobacco-growing region of China. Notably, significant pathogenic variation was observed within strains of the same sequevar, and no clear correlation was found between the sequevar type and pathogenicity. Using Oxford Nanopore sequencing, we analyzed 103 strains of tobacco R. pseudosolanacearum from different geographical origins and pathotypes. The pangenome of R. pseudosolanacearum is comprised of 9008 non-redundant genes, divided into a core genome (36%), accessory genome (48.7%) and isolate-specific genes (15%). Core genome functions were related to oxidation–reduction reaction process and DNA transcription regulation, while the accessory genome was linked to DNA recombination, integration, and transposition. SNP analysis revealed an average of 36,740 SNP loci per strain, indicating evolutionary purification with ka/ks value below 1. Phylogenetic analysis divided 99 strains into 4 main groups, with sequevars correlated to specific branches, reflecting evolutionary relationships. We identified 2226 genomic islands across the strains, with each strain containing 18–25 islands, primarily related to translation regulation, transposition, and transposase activity. Analysis of virulence factors using the virulence factors database (VFDB) highlighted 1252 virulence genes within these islands, with a significant portion (36.5%) linked to effector transport systems, predominantly the type III secretion system (66.7%). Each strain averaged 60 type III effector proteins, with RipBK and RipAZ2 unique to highly pathogenic strains. This study provides a comprehensive understanding of pan-genome of R. pseudosolanacearum causing tobacco bacterial wilt in China, providing valuable insights into virulence variation and environmental adaptation of the pathogen.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".