A chromosome-level genome assembly provides insights into the environmental adaptability and outbreaks of Chlorops oryzae.
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.
- ✓Reported values were directly comparable
- ✓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
- 🟡Could not use the authors’ exact input data
- 🟡A deviation arose in the data or preprocessing
- 🟡Overall, the reproduction showed a material discrepancy
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
DESCRIBED WELL ENOUGH + faithful 1:1 on the assembly-QC outputs. Approach P16: instead of re-running the infeasible full Canu v1.5 de-novo assembly + BLASR/Arrow/Pilon polishing + Hi-C scaffolding from raw reads (the hard 20%: days, hundreds of GB), I downloaded the authors' OWN deposited assembly GCA_020466095.1 (Cory_1.0) to «infra» and recomputed the Table-1 genome-QC stats on «our HPC»/SLURM. Today's fresh stats «job» reproduces BYTE-IDENTICAL to the prior run (FASTA sha256 confirmed identical): scaffold N50 117,565,011 bp byte-identical (= length of chromosome CM035807.1, proving the deposited file IS the paper's assembly), 4 chromosomes + GC 36.10 vs 36.09 exact, contig N50 +0.4%, genome size -0.37%, scaffold/contig counts within ~1.3% (consistent with GenBank submission filtering, NOT fabrication). BUSCO (C9) v5.7.1 = 96.9% eukaryota_odb10 / 95.7% insecta_odb10 vs reported 96.1% (within 0.8 pp despite v3->v5 jump); value from the prior COMPLETED «our HPC» run 2177556 because today's deterministic re-run (2219752) was blocked by a full shared «infra» group quota (documented in reproduction/outputs/PROVENANCE.txt). NO FABRICATION SIGNAL. NOT ATTEMPTED (hard 20%, scope.md): full de-novo Canu+Hi-C re-assembly, repeat content C8, gene annotation C11. All 9 in-scope assembly-QC claims reproduce. Grades provisional pending human audit (AUDIT.md).
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.
-
v1 current initial assessment Score 80assessed: 2026-06-15 ⛓ fcac4a9054f5
✎ I am an author of this paper
Updated or fixed a deposit, or is there an erratum? Ask us to re-run the metrics. We verify by email first; the new result is published as a new version with full history — nothing is overwritten.
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
- 2026-06-23
- Rubric version
- v1.0
- Assessed by
-
🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-15no 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 paper tests whether genomic features of Chlorops oryzae—particularly detoxification (cytochrome P450), thermal stress-response, and reproductive signaling genes—can explain the species' environmental adaptability and the recent increase in frequency of its outbreaks on rice.
- ★ A high-quality chromosome-level genome assembly of C. oryzae was generated using PacBio, Illumina, and Hi-C sequencing resource
- ★ HSP and antioxidant genes are relatively highly expressed in response to thermal stress, suggesting a role in environmental adaptability of C. oryzae finding
- ★ Juvenile hormone, 20-hydroxyecdysone, and insulin signaling pathways regulate vitellogenesis and ovarian development, linking reproduction to population maintenance/outbreaks finding
- ★ 69 cytochrome P450 genes were identified in the C. oryzae genome, classified into four major clans finding
- C. oryzae diverged from Ceratitis capitata approximately 186 million years ago finding
- ★ RNAi knockdown of vitellogenin (Vg) completely prevents ovary maturation finding
- Compared with the common ancestor of C. oryzae and C. capitata, the C. oryzae genome shows 561 expanded and 416 contracted gene families finding
- C. oryzae has fewer predicted P450 genes than other Diptera finding
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| Whole-genome sequencing and chromosome-level assembly | C. oryzae (whole organism) | none | assembly size, contig/scaffold N50, chromosome anchoring | PacBio Sequel, Illumina HiSeq X Ten, Hi-C |
| Genome completeness assessment | C. oryzae genome assembly | none | % complete single-copy orthologous genes | BUSCO v3.0.1 |
| Orthology and phylogenetic/divergence analysis | C. oryzae and 14 other insect species (6 orders) | none | single-copy orthologous genes, phylogenetic tree, divergence time | OrthoMCL, PhyML, mcmctree |
| Gene family expansion/contraction analysis | C. oryzae vs C. capitata and related species | none | number of expanded and contracted gene families | CAFE |
| Cytochrome P450 gene family identification and phylogenetics | C. oryzae genome, compared with D. melanogaster, L. cuprina, C. capitata | none | number of P450 genes, clan/clade classification | MEGA v7.0 (Neighbor-Joining tree) |
| Comparative transcriptomics (RNA-seq) | C. oryzae larvae | thermal stress (24°C, 33°C, 39°C) | differentially expressed transcripts, GO functional categories | — |
| qRT-PCR | C. oryzae larvae | thermal stress (24°C, 33°C, 39°C) | mRNA expression of HSP and antioxidant genes (HSPs, CAT, POD, SOD, GST) | — |
| RNAi knockdown | C. oryzae newly emerged adult females | dsRNA knockdown of Vg, Met, Kr-h1, Tai, InR, FOXO, TOR, PI3K, USP vs dsEGFP control | ovarian/oocyte development and maturation | — |
- – Chromosome-level genome assembled: 447.60 Mb, contig N50 1.17 Mb, scaffold N50 117.57 Mb, 93.22% of scaffolds anchored to 4 chromosomes, BUSCO complete 96.1%
- – 17,259 protein-coding gene models predicted; 86.12% functionally annotated 86.12%
- – C. oryzae diverged from C. capitata around 186 million years ago 186 Mya
- – 561 gene families expanded and 416 contracted relative to the common ancestor of C. oryzae and C. capitata 561 expanded / 416 contracted
- – 69 cytochrome P450 genes identified, falling into four major clans (CYP2, CYP3, CYP4, Mito) 69 genes
- ▲ HSP83, HSP70, HSP68, HSP67B2, HSP27, HSP23 and antioxidant genes SOD, GST, POD were significantly upregulated under high-temperature stress by qRT-PCR
- – Differentially expressed transcripts increased with temperature difference: 1519 up/1823 down (24°C vs 33°C), 1487 up/6996 down (24°C vs 39°C), 1641 up/6232 down (33°C vs 39°C)
- ▼ RNAi of Vg completely prevented ovary maturation; knockdown of Met, Kr-h1, InR, FOXO, TOR, PI3K, USP impaired yolk deposition/ovarian development; Tai knockdown had no effect
- other 447,595,289 bp genome size (final assembled genome size)
- other Contig N50 = 1,171,122 bp; Scaffold N50 = 117,565,011 bp (assembly contiguity)
- other BUSCO complete = 96.1% (genome completeness)
- other 93.22% of scaffolds anchored to chromosomes (Hi-C chromosome anchoring)
- count 17,259 predicted gene models; 14,863 (86.12%) functionally annotated (gene prediction and annotation)
- count 69 cytochrome P450 genes (P450 gene family size)
- other ~186 million years divergence time from C. capitata (phylogenetic divergence estimate)
- count DEGs: 1519 up/1823 down (24 vs 33°C); 1487 up/6996 down (24 vs 39°C); 1641 up/6232 down (33 vs 39°C) (thermal stress differential expression)
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 paper reports a chromosome-level genome assembly of Chlorops oryzae built with PacBio long reads, Illumina short reads, and Hi-C chromatin contact data, supplemented by gene annotation and comparative genomics. Transcriptome profiling across three temperature treatment groups identified differentially expressed genes (method not named), with qRT-PCR used for validation across three biological replicates. Phylogenetic relationships were inferred by maximum likelihood (PhyML) and neighbor-joining (MEGA v7.0) methods. RNAi knockdown experiments assessed effects on ovarian development through qualitative phenotypic observation.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Differential expression analysis (specific tool and statistical model not stated) | Pairwise transcriptome comparisons across temperature groups: 24 °C vs 33 °C, 24 °C vs 39 °C, and 33 °C vs 39 °C | — | not stated |
| qRT-PCR relative quantification (specific statistical test not stated) | Validation of stress-response and antioxidant gene expression across temperature treatment groups | 3 biological replicates per gene | not stated |
| Maximum likelihood phylogenetic inference (PhyML, 100 bootstrap replicates) | Species-level phylogenetic tree inferred from 2298 single-copy orthologous genes across 15 insect species | 15 insect species, 2298 single-copy orthologous genes | na |
| Neighbor-joining (NJ) with Poisson correction (MEGA v7.0, 1000 bootstrap replicates) | Cytochrome P450 gene family phylogenetic tree across C. oryzae, D. melanogaster, L. cuprina, and C. capitata | 69 C. oryzae P450 genes plus sequences from three other Diptera | na |
| CAFÉ probabilistic model of gene family size change | Gene family expansion and contraction in C. oryzae relative to related species | — | not stated |
| BUSCO completeness assessment (v3.0.1) | Evaluation of genome assembly completeness against eukaryotic single-copy ortholog set | — | na |
-
The differential expression tool and statistical model used for RNA-seq are not named in the main text↳ Could also: DESeq2 (negative-binomial Wald test), edgeR (quasi-likelihood F-test), or limma-voom are all standard, widely-cited tools for RNA-seq differential expression — Naming the specific tool and version allows readers to understand the underlying statistical model, normalization strategy, and dispersion estimation approach, and enables full reproduction of results
-
The number of biological replicates per group for the RNA-seq experiment is not reported in the main text↳ Could also: Stating replicate counts per condition (e.g., n = 3 biological replicates per temperature group) alongside the sequencing depth is standard practice — Replicate number directly governs the power of differential expression tests; it is typically required by journals and allows readers to evaluate the statistical reliability of up- and down-regulation calls
-
qRT-PCR results are presented as log2 ratios in a heat map without dispersion measures or a named statistical test↳ Could also: Presenting mean ± SD with individual data points and a stated test — e.g., one-way ANOVA with Tukey HSD post-hoc, or Kruskal-Wallis with Dunn's test — is also widely used for multi-group qRT-PCR comparisons — With n = 3 biological replicates, showing a dispersion measure and a named test allows readers to assess variability and the formal basis for significance statements across groups
-
Multiple pairwise temperature comparisons were made without a stated multiplicity correction↳ Could also: A single one-way ANOVA (or Kruskal-Wallis for non-parametric data) with a post-hoc test such as Tukey HSD or Dunn's correction applied across the three comparisons would also be applicable — Controlling the family-wise error rate or FDR across simultaneous pairwise comparisons reduces the probability of false-positive significance declarations, particularly when many genes are tested
-
RNAi knockdown effects on ovarian development were assessed qualitatively via representative microscopy images↳ Could also: Quantitative endpoints — such as ovary length, oocyte count, or vitellogenin protein level by western blot — with stated n per group and a formal test (e.g., Dunnett's test vs. dsEGFP control) would also be applicable — Quantitative measures with dispersion and a statistical test allow effect magnitude and inter-individual variability to be communicated alongside phenotypic images, and support comparison across knockdown conditions
-
The NJ method with Poisson correction was used for the P450 gene family phylogeny↳ Could also: Maximum likelihood (e.g., IQ-TREE with automatic substitution model selection by BIC) or Bayesian inference (MrBayes) with an amino acid substitution model selected by AIC/BIC is also commonly used for gene family phylogenies — Model-based methods can better account for among-site rate variation and long-branch attraction; posterior probabilities or SH-aLRT branch support complement bootstrap values and are increasingly expected in gene-family phylogenetics
Citation network
Where this publication sits in the reproducibility-weighted citation graph — what it is built on, and what is built on it. Citation data from OpenAlex.
No assessed neighbours yet — the network grows as more papers are assessed.
Data lineage
The datasets this paper uses (text-mined from the full text via Europe PMC), and which other assessed papers stand on the same data. A shared dataset is a factual link — not a judgement.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — PMID 36028584 (Chlorops oryzae chromosome-level genome)
Paper: Zhou et al. 2022, Commun Biol 5:881. doi:10.1038/s42003-022-03850-7. PMCID PMC9418232. Assembly tool cited: Canu (github.com/marbl/canu).
Deposited artifacts (resolved)
- Genome assembly: GenBank
JAIPUU000000000= GCA_020466095.1 (nameCory_1.0), submitter Hunan Agricultural University (matches authors). BioProject PRJNA728371. NCBI precomputed: total 445,960,279 bp · contig N50 1,175,937 · scaffold N50 117,565,011 · 4 chromosomes · 3450 contigs · 1561 scaffolds · 125× coverage. - Raw genome reads: SRA SRR14340331 (PacBio), BioProject PRJNA728371. Hi-C data deposited.
- Transcriptome: SRR75284xx / SRR75xxxxx series (multiple BioProjects) for annotation.
Reported pipeline-derived results (Table 1, "Features of the C. oryzae genome assembly")
| # | Feature | Reported value | Pipeline |
|---|---|---|---|
| C1 | Genome size (bp) | 447,595,289 | Canu+polish assembly |
| C2 | Number of chromosomes | 4 | Hi-C scaffolding |
| C3 | Number of contigs | 3407 | Canu+polish |
| C4 | Contig N50 (bp) | 1,171,122 | Canu+polish |
| C5 | Number of scaffolds | 1575 | Hi-C scaffolding |
| C6 | Scaffold N50 (bp) | 117,565,011 | Hi-C scaffolding |
| C7 | GC content (%) | 36.09 | sequence stat |
| C8 | Repeat (%) | 57.38 | RepeatModeler+RepeatMasker |
| C9 | BUSCO (% complete) | 96.1 | BUSCO v3.0.1, eukaryota set |
| C10 | % scaffolds in chromosomes | 93.22 | Hi-C scaffolding |
| - | Gene models | 17,259 | EVM annotation pipeline |
IN SCOPE (reproduced by recomputing QC outputs from the deposited assembly)
P16 framing: run standard third-party QC tools on the paper's own deposited genome.
- C1, C3, C4, C5, C6, C7, C2, C10 — pure assembly sequence statistics, computed deterministically from GCA_020466095.1 FASTA + assembly_report (stdlib python).
- C9 (BUSCO) — re-run BUSCO (v5.7.1, eukaryota_odb10 + insecta_odb10) on the deposited genome. Version differs from paper's v3.0.1, so a tolerance/qualitative comparison, not byte-identical.
OUT OF SCOPE (the hard ~20%, not attempted — justified)
- Full Canu de-novo re-assembly + Hi-C scaffolding from raw reads (SRR14340331 + Hi-C): days of compute, hundreds of GB, BLASR/Arrow/Pilon/HiC-Pro multi-tool chain with Canu v1.5 (old, grid-engine params). Not feasible under the 80/20 budget; the deposited assembly is the canonical output and the right object to QC.
- C8 Repeat % (57.38) — RepeatModeler de-novo library build + RepeatMasker on a 446 Mb genome (many hours–days, RepBase license). Not attempted.
- Gene count (17,259) — full EVM annotation pipeline (PASA/Augustus/GeneWise/ homology + RNA-seq evidence). Multi-day, multi-tool. Not attempted.
- Wet-lab / RNAi / comparative-evolution / DEG results — non-pipeline or out of the assembly-QC scope.
Note on size discrepancy
Paper Table 1 genome size = 447,595,289 bp; NCBI-deposited GCA_020466095.1 total = 445,960,279 bp (Δ ≈ 1.64 Mb, 0.37%). Expected: GenBank submission filters short/ contaminant/adapter sequences vs the authors' pre-submission assembly. Scaffold N50 is byte-identical (117,565,011), confirming same assembly. We compute our own number from the FASTA and report both.
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.
This is a strong, fair reproduction: the agent recomputed all 9 in-scope Table-1 QC statistics from the authors' deposited assembly GCA_020466095.1, and the byte-identical scaffold N50 (117,565,011 bp = len(CM035807.1)) plus exact chromosome count and GC confirm the deposited file is the paper's assembly. The only deltas — genome size 0.37%, contigs 1.3%, BUSCO 0.8pp — are on the input/preprocessing side (GenBank submission filtering, contig definition, BUSCO version drift) and all reconcile to NCBI precomputed stats; no fabrication signal. It is q8-yellow rather than green because it verifies stats on the authors' own output rather than regenerating the Canu/Hi-C pipeline, and the two pipeline-heavy claims (repeat content, 17,259 genes) were out of scope and unverified.
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.
Are you an author? We would genuinely like to hear from you — to clarify the record, add data or code, re-run the pipeline after an accession update, and publish your response right next to the assessment. Everything here is open and auditable.
🚩 Report an error in this record
Spotted something wrong — a verdict you’d contest, a data or value error, or a private detail that slipped through? Tell us, with a short justification. Authors and readers are equally welcome to write in; we review every report.
Prefer email, or the form below not working? Contact us at support@doesitreproduce.com.
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.