Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac<
The main results reproduced: recomputed values matched the published ones within tolerance.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓Same input data as the authors
- ✓Reported values were directly comparable
- ✓No relevant deviation in data/preprocessing
- ✓No authors-side cause for any deviation
- ✓Reported values are derivable from the shared data
- ✓Any deviation was negligible
- ✓The central claim held under reproduction
- ✓Overall, the reproduction was clean
- Every checked point held up.
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
1:1 reproduction of the paper's primary computational result. Ran the named tool pyani v0.2.11 (ANIm; MUMmer 3.23 + BLAST+ 2.17.0) on the paper's own 11 deposited RefSeq assemblies (PRJNA794971) plus the P. aroidearum reference and 4 near-neighbour Pectobacterium species, all on «our HPC» («job»). C1: the 11 konjac isolates + reference form one cluster at >=98.30% ANI (all >95%) => species P. aroidearum, reproducing the central taxonomic claim. C1b: every near-neighbour species is <=90.86% ANI (<95%), confirming the 95% boundary separates them. C2a (genome size 4,865,541-5,057,072 bp) and C2b (GC 51.6-51.9%) reproduced EXACTLY from the deposited FASTA. Paper is described well enough; named third-party tool directly applicable (P16). NOT attempted (out of scope / unreproducible-as-specified): annotation-derived counts C2c/d/e, pangenome C3 (tool/version unpinned), virulence C4 (DB unpinned). Dataset PRJNA794971 profiled: 11/11 complete single-contig genomes, open RefSeq, sizes match Table 1 to the byte; grade A. Solver gotchas handled: front1 login-node tmpfs is 50M/full (built conda env on a compute node's 750G node-local /tmp); conda otherwise pulls python 3.14 + matplotlib>=3.9 which breaks pyani 0.2.x at import (pinned python=3.8 + matplotlib-base<3.9).
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
Assessment versions
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
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v1 current initial assessment Score 100assessed: 2026-06-21 ⛓ ea80c4dec884
✎ I am an author of this paper
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Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-21
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-21no human curator yet
- Last updated
- 2026-08-05
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
Deep full-text extraction
Model: sonnetThe study aims to definitively determine the causal agent of konjac (Amorphophallus konjac) soft rot using genomic data and to characterize the taxonomy, synteny, pangenome plasticity, and virulence factor variation of this pathogen through comparative genomics.
- ★ The causal agent of konjac soft rot in China is Pectobacterium aroidearum, confirmed via in vitro/in vivo pathogenicity tests, ANI, dDDH, and phylogenomic analysis. finding
- ★ 11 complete P. aroidearum genomes were sequenced and assembled via hybrid Nanopore/Illumina sequencing. method
- ★ Synteny analysis reveals considerable chromosomal inversions among P. aroidearum strains, one caused by homologous recombination of the ribosome operon. finding
- ★ The pangenome of P. aroidearum is open, with accessory genes enriched for replication, recombination, and repair functions. finding
- ★ Type IV and type VI secretion systems show strain-level variation while plant cell wall degrading enzymes (PCWDEs) remain conserved. finding
- ★ Sequence analysis provides evidence for the presence of a type V secretion system in Pectobacterium. finding
- P. aroidearum QJ036 exhibits a broader host range than previously reported, causing rot in sweet potato, jicama, yacon, and taro. finding
- ★ Three strains named P. carotovorum subsp. carotovorum (PC1, PCCS1, PCC21) cluster within P. aroidearum's clade and are likely misnamed. finding
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| in vitro pathogenicity assay (tuber slice inoculation) | Amorphophallus konjac tubers | bacterial inoculation (11 isolates) | soft rot symptom formation | — |
| in vivo pathogenicity assay (pin-prick inoculation) | 6-month-old konjac seedlings (stems) | bacterial inoculation (strain QJ036) | stem rot and wilting symptoms | — |
| pectinolytic activity assay | bacterial isolates on crystal violet pectate (CVP) medium | none | pit/cavity formation | — |
| 16S rRNA gene sequencing and BLAST analysis | 11 bacterial isolates | none | sequence identity to P. aroidearum reference | — |
| whole-genome sequencing and hybrid de novo assembly | 11 P. aroidearum isolates | none | complete genome sequences | Nanopore PromethION and Illumina NovaSeq PE150 |
| ANI and digital DNA-DNA hybridization (dDDH) | 64 Pectobacterium genomes (11 new + 53 from GenBank) | none | pairwise sequence identity for species delineation | pyani v0.2.11; Genome-to-Genome Distance Calculator 3.0 |
| whole-genome synteny/alignment analysis | P. aroidearum genomes | none | chromosomal rearrangements/inversions | progressiveMauve; D-Genies; BRIG |
| pangenome and COG functional enrichment analysis | 64 Pectobacterium genomes / 14 P. aroidearum genomes | none | core/accessory gene counts, functional category enrichment | Roary; eggNOG-mapper v2.1.4; Fisher's exact test |
- – All 11 isolates caused typical soft rot symptoms on konjac tubers in vitro and formed pits on CVP medium
- ▲ 16S rRNA genes of all 11 isolates share high identity with P. aroidearum reference NR_159926 ≥99% identity
- – Strain QJ036 caused stem rot and wilting in seedlings within 2 days in vivo; controls showed no symptoms
- ▲ Clade IV strains (including P. aroidearum L6, PC1, PCCS1) show ANI and dDDH above species delineation cutoffs ANI >95%; dDDH >70%
- – Pectobacterium pangenome (64 genomes) contains a small proportion of core genes relative to total pangenome, indicating an open pangenome 2,228 core genes / 19,698 total (11.31%)
- – P. aroidearum pangenome (14 genomes) has a larger core gene proportion but remains open with continued gene accumulation 6,630 total genes; 3,575 core (53.92%)
- – QJ036 caused rot symptoms on sweet potato, jicama, yacon, and taro tuber slices, expanding known host range
- – Genomic inversion between QJ036 and QJ002 borders coincide with ribosome operon locations, implicating homologous recombination
- other ≥99% 16S rRNA identity (species identification of konjac soft rot isolates as P. aroidearum)
- other ANI >95%, dDDH >70% (species delineation cutoff met among clade IV strains)
- count 2,228 core genes / 19,698 pangenome genes (11.31%) (Pectobacterium genus pangenome analysis)
- count 6,630 pangenome genes; 3,575 core genes (53.92%) (P. aroidearum pangenome analysis)
- other genome size range 4,865,541–5,057,072 bp (P. aroidearum genome assemblies)
- other GC content 51.6%–51.9% (P. aroidearum genome assemblies)
- count CDS range 4,277 (QJ311) to 4,469 (AK042) (protein-coding gene counts across strains)
- count accessory genes per strain range 701 (PC1) to 898 (QJ003) (P. aroidearum pangenome accessory gene variation)
Statistical methods review
Model: sonnetA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
This is a comparative/functional genomics study of Pectobacterium aroidearum strains isolated from konjac, combining in vitro/in vivo pathogenicity assays with whole-genome sequencing, phylogenomics (parsimony and maximum-likelihood trees), average nucleotide identity/digital DNA-DNA hybridization for species assignment, pangenome analysis (Roary), and COG functional enrichment. The only inferential statistical test described is Fisher's exact test for COG category enrichment, with p-values adjusted for multiple comparisons. Most other results (genome features, ANI/dDDH values, phylogenetic placement, pangenome composition) are reported descriptively or against established cutoff thresholds rather than through hypothesis tests.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Fisher's exact test | COG functional category enrichment analysis of protein-coding genes (e.g., accessory genes enriched in replication, recombination, and repair) | — | not stated |
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Functional (COG) enrichment was assessed with Fisher's exact test corrected by the Benjamini-Hochberg method.↳ Could also: A hypergeometric test or a gene-set enrichment approach (e.g., GSEA-style permutation testing) could also be used — These are standard alternatives for categorical enrichment testing and can be preferred when category sizes are large or when a continuous ranking of genes (rather than a binary presence/absence split) is available, potentially increasing sensitivity.
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Species assignment relied on fixed ANI (>95%) and dDDH (>70%) cutoff thresholds combined with tree topology.↳ Could also: Bootstrap or jackknife resampling of ANI/dDDH estimates, or a probabilistic/model-based species delimitation method (e.g., using confidence intervals around ANI values), could also be reported — Adding a measure of uncertainty around the ANI/dDDH point estimates would let readers gauge how close values are to the delineation threshold, which is informative near borderline cases.
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Phylogenetic relationships were inferred using a parsimony method (kSNP3) and a maximum-likelihood method (FastTree) without reported bootstrap or posterior support values in the described results.↳ Could also: Bayesian phylogenetic inference (e.g., MrBayes or BEAST) with posterior probabilities, or standard bootstrap resampling (e.g., 100-1000 replicates) for the ML tree, could also be applied — Support values quantify confidence in individual branches/clades, which can strengthen claims about monophyletic grouping such as the konjac pathogen clade.
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Pathogenicity and pectinolytic assays were repeated at least twice independently and reported as consistent/qualitative outcomes (symptom presence/absence).↳ Could also: Quantitative scoring of lesion size or symptom severity across a larger number of biological replicates, summarized with a dispersion measure (SD, SEM, or CI) and compared statistically (e.g., t-test or ANOVA across isolates/timepoints), could also be used — Quantitative, replicate-based comparisons allow formal statistical inference about differences in virulence between isolates or conditions, beyond descriptive agreement across two repeats.
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Pangenome 'openness' was inferred qualitatively from the shape of the core/pangenome accumulation curves as more genomes were added.↳ Could also: Fitting Heaps' law (or a similar power-law/exponential decay model) to the pangenome accumulation data and reporting the fitted exponent with a confidence interval could also be done — A fitted openness parameter with an interval estimate gives a quantitative, comparable measure of pangenome openness rather than a qualitative visual trend.
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Multiple-testing correction (Benjamini-Hochberg) was applied only to the COG enrichment analysis.↳ Could also: If additional comparisons were made across gene families, secretion-system presence/absence, or PCWDE conservation across the 14 genomes, a similar FDR or family-wise correction (e.g., Bonferroni) could also be applied to that broader set of comparisons — Extending multiplicity control to any additional comparison families would keep the overall false-positive rate consistent across all statistical claims in the study.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-35910650
Paper: Zhang Y, Chu H, Yu L, He F, Gao Y, Tang L. Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac. Front Microbiol. 2022;13:868709. DOI 10.3389/fmicb.2022.868709 · PMID 35910650 · PMCID PMC9326479.
Named code artifact (BRIEF): https://github.com/widdowquinn/pyani (pyani v0.2.11). This is a third-party tool (per P16, applying an existing tool to the paper's own data is an equally valid reproduction). pyani computes Average Nucleotide Identity.
Data: BioProject PRJNA794971 — 11 newly sequenced P. aroidearum genomes (Nanopore PromethION + Illumina NovaSeq, hybrid assembly, "Complete Genome"). Resolved to 11 GenBank/RefSeq assemblies (GCF_024498675.1 … GCF_024498875.1), 22 SRA runs (11 strains × 2 platforms). Plus 53 publicly downloaded Pectobacterium reference genomes (listed in Supplementary Table; 64 total in the genus analysis).
In-scope (pipeline-derived, attempted)
| # | Result | Pipeline / tool named in paper | Reproducible? |
|---|---|---|---|
| C1 | ANI species delineation: the 11 konjac isolates are P. aroidearum; all clade-IV pairwise comparisons exceed the 95% ANI species threshold (Results "Taxonomy"; Table 1 / Suppl. Table 4) | pyani v0.2.11, ANIm method | PRIMARY TARGET — directly re-runnable with the named tool on the deposited assemblies. The strongest 1:1 result. |
| C2 | Genome characteristics (Table 1): size 4,865,541–5,057,072 bp; GC 51.6–51.9%; CDS 4,277–4,469; tRNA 77; rRNA 22 | assembly stats / annotation (NCBI PGAP for RefSeq) | Partially checkable directly from the deposited assemblies (size, GC, contig count, RefSeq CDS/tRNA/rRNA counts). Annotation tool not pinned by authors → treat as provisional supporting evidence. |
| C3 | Pangenome: P. aroidearum (14 strains) core 3,575 / pan 6,630; genus (64 strains) core 2,228 / pan 19,698 | (Roary-class; tool/version not clearly pinned) | Secondary — attempt only if reference set fully resolvable; high parameter sensitivity. |
Out of scope (not pipeline / not attempted, or weakly specified)
- Wet-lab: DNA extraction, sequencing, pathogenicity assays — not computational.
- Synteny (progressiveMauve / D-Genies dot plots, chromosomal inversions) — visual/ qualitative; no single numeric claim to grade 1:1.
- Phylogenetic trees (kSNP3 v3.1.2, FastTree 2.1.11) — topology/clade membership is reproducible but graded qualitatively, not as a number; secondary.
- Virulence factors (TXSScan/MacSyFinder, SecReT6, InterProScan, IslandViewer4, BLAST+ for PCWDE = 21 genes/strain) — multiple unpinned external web servers; PCWDE count is a candidate secondary check (BLAST+ is reproducible) but DB versions undefined → provisional at best.
- dDDH >70% (Genome-to-Genome Distance Calculator web server) — external web service, not locally reproducible deterministically.
Reproduction strategy for C1 (primary)
- Download the 11 deposited assemblies (GCF_024498675.1 … _875.1) + a reference set anchoring the species boundary: the P. aroidearum type/reference strain and a few near-neighbour Pectobacterium species (e.g. P. carotovorum, P. brasiliense, P. parmentieri) — all onto «infra» via front1.
- Run pyani anim (MUMmer/nucmer) on the genome FASTAs on a «our HPC» compute node.
- Read the percentage-identity matrix; verify: (a) all 11 konjac isolates are mutually >95% ANI (one species) and >95% to the P. aroidearum reference, and (b) near-neighbour species fall below 95%. This reproduces the taxonomic assignment that is the paper's central computational claim.
Grade basis: the paper states "> 95%" rather than itemising every pairwise value in the main text (values in Suppl. Table 4), so C1 is graded against the threshold claim and species-assignment conclusion, not against per-cell decimals.
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
An automated assessment. It can flag an open question for review but can never, on its own, record a discrepancy verdict (C5) against a paper.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
1:1 reproduction of the primary result. The central taxonomic claim (P. aroidearum species assignment via >95% ANI) was reproduced exactly using the authors' own named tool (pyani v0.2.11 ANIm) on their own deposited RefSeq assemblies: ≥98.30% ANI within clade vs ≤90.86% to near-neighbours, with genome size matching to the byte and GC rounding exactly to Table 1. No deviation sits on the authors' side for any attempted value. The only limitation is on method specification: annotation counts, the pangenome, and PCWDE virulence counts were not gradable because the authors did not pin the annotation tool, Roary-class version, or reference DB — these are secondary and non-deterministic, not discrepancies, so the overall judgement remains green.
Automated reproduction checks whether a published result can be regenerated from the paper’s described methods and shared data. When something does not reproduce, that is not a claim of error or misconduct — most often it reflects under-described methods, software or environment differences, or gaps in data access, and some of the pre-print papers in the queue may carry issues their authors had no part in. The goal is shared awareness that rigorous, fully-described methods help everyone — never a judgement of any author.
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Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.