The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary
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
Described well enough; 1:1. P16 reproduction: ran the brief's code link (KorfLab/Assemblathon assemblathon_stats.pl, commit 160b94c) on the authors' OWN deposited assembly GCA_928718305.1 (ENA PRJEB47619, assembly FASTA sha256 fcbb0717..., 288 scaffolds, 257,967,262 bp). All four headline genome-assembly statistics regenerate EXACTLY on a clean re-run this session («our HPC» «job», node n096, perl 5.36 / Debian 12; environment.lock captured): total size 257,967,262 bp (=258 Mb), scaffold N50 22,406,985 bp (=22.4 Mb), scaffold L50 5, and 11 chromosome-scale scaffolds (>=10 Mb). NOT attempted: (a) the initial MaSuRCA 3.3.1 contig assembly (intermediate never deposited; multi-day de-novo run = the hard 20%); (b) BUSCO completeness (version-fragile); (c) venom-peptide annotation/phylogenetics (manual+wet-lab). Grades provisional pending human audit.
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: 2026-06-15 ⛓ 3a699206e9e8
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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
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🤖 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: sonnetBy sequencing and assembling the genome of the ant Tetramorium bicarinatum, the study investigates how venom peptide genes (vpg) are organized, structured, and regulated to understand the genomic mechanisms underlying the evolution and diversification of myrmicitoxins.
- ★ 44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters. finding
- ★ The tandem organization and ML evolutionary analysis of vpg sequences are consistent with evolution by local duplication of ancestral genes within each precursor family. mechanism
- ★ The two/three-exon gene structure of vpg is conserved after duplication events, but promoter regions are the least conserved parts even among highly identical gene sequences. finding
- ★ Enhancer sequences were likely not duplicated along with the genes but instead recruited from surrounding genomic regions. mechanism
- ★ Most vpg are highly expressed in venom glands, with one gene or gene group dominating expression within each precursor family. finding
- ★ Several transcription factor (TF) genes are highly expressed in venom glands and show hot spots of GATA binding sites in vpg promoters. finding
- ★ A high-quality chromosome-level genome assembly of T. bicarinatum was produced (258 Mb, 11 chromosomes) and made available as a resource. resource
- Phase-1 or phase-2 introns are specific features of the A1 and A3 gene families that encode disulfide-bonded peptides, whereas A4 genes have phase-0 introns. finding
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| Whole-genome sequencing and assembly (contig + Hi-C scaffolding) | Tetramorium bicarinatum (whole organism/genome) | none | assembly size, N50, L50, BUSCO completeness, chromosome-level scaffolding | MaSurCa; genomescope2; Hi-C |
| BLAST homology search | T. bicarinatum assembled genome vs. 37 previously identified venom transcripts | none | identification and chromosomal localization of 44 venom peptide genes (vpg) | BLAST |
| Gene structure annotation/prediction | vpg loci across 4 chromosomes | none | exon/intron number, phase, splice sites, pseudogene identification | Maker gene predictor |
| SRA transcriptomic read mapping | venom gland cells | none | expression level of vpg and pseudogenes, confirmation of transcript splicing/mRNA production | SRA alignment |
| Maximum likelihood (ML) evolutionary/phylogenetic analysis | vpg coding sequences across precursor families | none | evolutionary relationships supporting local gene duplication | — |
| Promoter sequence analysis | vpg promoter regions | none | TATA box position and consensus sequence, promoter conservation | — |
| Transcription factor binding site (TFBS) search | vpg promoter regions | none | identification of GATA and other TF binding site hot spots | — |
| Functional annotation via database homology (UniProtKB/Swiss-Prot) | genes flanking vpg clusters | none | identification of neighboring functional genes (e.g., Corin, octopamine receptor, otubain-like) | UniProtKB_refprot/Swiss-Prot |
- – 44 vpg identified across four chromosomes, clustered in tandem repeats (e.g., 13 A1 genes over 150 kb on chromosome 9; 15 C1 genes plus 3 A3 genes on chromosome 6)
- – Scaffolded genome assembly quality improved over contig assembly: size decreased from 276.3 Mb to 258 Mb, N50 increased from 3.4 Mb to 22.4 Mb, L50 improved from 24 to 5
- ▲ BUSCO completeness high in both assemblies (only 6-7 fragmented and 5 missing of 1,658 genes); duplicated genes dropped from 51 to 18 after scaffolding, reflecting removal of retained haplotigs
- – Ten new venom peptide precursor genes identified that were not found in prior proteo-transcriptomic study, expressed in venom gland
- – Multiple pseudogenes detected within vpg clusters (e.g., frameshift and start-codon-loss pseudogenes in A1, A2, and A4 families), some still transcribed at low levels
- – A1 gene first introns are phase 2, C1/A3 genes show phase-1 introns, while A4 genes (MYRTX A4-Tb11a/b) uniquely show phase-0 introns among disulfide-bonded peptide genes
- – Alternative splicing of MYRTX A1-Tb18a produces two transcripts; only the single-disulfide-bond peptide (Tb7b) is detected by mass spectrometry, homologous to a confirmed T. africanum peptide
- – TATA box consensus sequences and spacing (typically -17 to -23 bp from TSS) identified for each gene family (A1, A2, B1, B2, A4, C1)
- count 44 venom peptide genes (vpg) across 4 chromosomes (total vpg identified by BLAST)
- other N50 = 3.4 Mb, L50 = 24 (contig assembly); N50 = 22.4 Mb, L50 = 5 (scaffolded) (genome assembly quality metrics)
- count 6 fragmented and 5 missing genes out of 1,658 (contig); 7 fragmented and 5 missing out of 1,658 (scaffolded) (BUSCO completeness score)
- other assembly size 276.3 Mb (contig) vs. 258 Mb (scaffolded); expected genome size 250 Mb (genome size vs. genomescope2 estimate)
- count duplicated genes reduced from 51 to 18 (effect of scaffolding on haplotig removal)
- other 13 A1 genes spanning 150 kb (22,401,914–22,552,361 bp) on chromosome 9 (A1 family gene cluster size)
- other Corin homolog match evalue = 0 (A1Z709) (functional annotation of gene between A1 vpg)
- other second exon of A1 genes averages 26 bp (range 13–42 bp); C1 first exon averages 282 bp with intron averaging 446 bp; MYRTX C1-Tb17o intron = 3473 bp (vpg exon/intron length statistics)
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 single-species genome assembly and annotation study of Tetramorium bicarinatum. The primary analytical outputs are genome quality metrics (BUSCO completeness, N50/L50, k-mer content), BLAST-based gene identification, structural gene annotation, maximum-likelihood (ML) phylogenetic inference on venom peptide gene (vpg) sequences, RNA-seq-based expression level comparisons, and motif scanning of promoter regions for transcription factor binding sites. No classical inferential statistics (e.g., hypothesis tests with p-values) are applied to experimental groups; results are reported as descriptive metrics, BLAST E-values, and qualitative expression comparisons. The paper is cut off before the full evolutionary analysis and expression quantification methods are described.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| BUSCO completeness scoring (Benchmarking Universal Single-Copy Orthologs) | Assembly quality assessment — contig and scaffolded assemblies | 1,658 BUSCO genes queried | na |
| BLAST sequence similarity search (E-value thresholding) | Identification of vpg in assembled genome; functional annotation of flanking genes | 37 previously published venom transcript sequences used as queries | not stated |
| Maximum-likelihood (ML) phylogenetic analysis | Evolutionary analysis of vpg sequences across precursor families (referenced in abstract and results; full methods section not included in provided text) | 44 vpg identified; exact alignment size not stated in provided text | not stated |
| RNA-seq read mapping / expression level comparison (method not fully described in provided text) | Expression of vpg in venom glands; comparison across gene family members | null | not stated |
| Transcription factor binding site (TFBS) motif scanning / TATA box consensus identification | Promoter regions of vpg families; GATA site hotspot identification | null | not stated |
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Expression differences among vpg family members are described qualitatively (e.g., 'one gene or group of genes is much more highly expressed in each family')↳ Could also: Formal differential expression analysis using DESeq2 or edgeR with biological replicates could also be applied to quantify expression differences and provide adjusted p-values and fold-change estimates — Statistical testing with FDR correction would allow readers to distinguish expression differences that exceed expected sampling variation from those that do not, and would provide a reproducible threshold for 'highly expressed'
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Maximum-likelihood phylogenetic inference is used for the evolutionary analysis of vpg sequences↳ Could also: Bayesian phylogenetic inference (e.g., MrBayes, BEAST) could also be applied to the same alignments — Bayesian methods provide posterior probability support values rather than bootstrap values and can incorporate more flexible substitution models; presenting both approaches can increase confidence in topological conclusions
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Transcription factor binding sites (TATA boxes, GATA sites) are identified by consensus motif scanning and described as 'hot spots'↳ Could also: Formal motif enrichment analysis (e.g., HOMER, MEME-ChIP, or AME) comparing vpg promoters against a background set of non-venom gene promoters could also be applied — Enrichment testing provides a statistical measure of whether binding site density in vpg promoters exceeds what is expected by chance, which would strengthen conclusions about regulatory specificity
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Assembly quality is assessed using BUSCO completeness scores and N50/L50 metrics↳ Could also: Additional quality assessment with QUAST (against a related reference genome) or Merqury (k-mer-based quality value estimation) could also be reported alongside BUSCO — Complementary metrics address different quality dimensions; QUAST captures structural accuracy relative to a reference while Merqury provides base-level accuracy estimates independent of annotation
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Sequence identity between pseudogene regions and active gene introns/exons is reported as single percentage values (e.g., '85% and 78% identity with intron 1')↳ Could also: Pairwise distance matrices or dN/dS (Ka/Ks) ratios could also be computed across all paralogous vpg pairs to quantify divergence rates and detect signatures of selection — dN/dS analysis would allow a neutral description of whether synonymous and nonsynonymous substitution rates differ across gene regions, informing the evolutionary interpretation of conserved coding versus divergent promoter sequences
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Intergenic region lengths are reported descriptively as ranges (e.g., '2600 bp to 11,600 bp')↳ Could also: Summary statistics including median and interquartile range, or a distribution plot, could also accompany range reporting for intergenic distances — Ranges are sensitive to outliers; median and IQR more robustly describe the typical intergenic spacing, which is relevant to conclusions about tandem repeat organization
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.
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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 38245722 (Tetramorium bicarinatum genome)
Paper: "The genome of the ant Tetramorium bicarinatum reveals a tandem
organization of venom peptides genes..." BMC Genomics 2024, DOI 10.1186/s12864-024-10012-y.
Code link in brief: https://github.com/KorfLab/Assemblathon (the
assemblathon_stats.pl assembly-statistics tool — a third-party tool, P16).
Data: ENA PRJEB47619 → deposited assembly GCA_928718305.1
(Tetramorium_bicarinatum_1.0), chromosome-level, WGS set CAKMUF01.
Reproduction strategy (P16)
This is a genome-assembly paper. Its headline pipeline-derived results are the
assembly summary statistics (total size, scaffold N50, L50, scaffold count).
The named code is a generic assembly-stats tool. The faithful reproduction is to
download the authors' own deposited assembly FASTA (GCA_928718305.1) and run
assemblathon_stats.pl on it, then compare the regenerated statistics to the
values printed in the paper. This is exactly the P16 "third-party tool on the
paper's own data" case and is fully valid.
In scope (attempted)
| # | Reported result | Pipeline | Reproducible? |
|---|---|---|---|
| C1 | Final assembly total size 258 Mb | assembly FASTA → assemblathon_stats | YES — FASTA deposited (GCA_928718305.1; ENA base_count 257,967,262 bp) |
| C2 | Scaffold N50 = 22.4 Mb | assemblathon_stats | YES |
| C3 | Scaffold L50 = 5 | assemblathon_stats | YES |
| C4 | 11 chromosomes | curated count of chromosome-scale scaffolds | partial — count chromosome-scale (CM/OV) scaffolds in the deposited set |
Out of scope / not attempted (and why)
- Initial MaSuRCA contig assembly (276.3 Mb, N50 3.4 Mb, L50 24): the raw/ intermediate contig assembly was not deposited (only the final scaffolded assembly GCA_928718305.1 is public). Re-running MaSuRCA 3.3.1 + 3D-DNA Hi-C scaffolding from raw reads (ERR8263729 ONT, ERR8263730 Hi-C, ERR8263731 Illumina) is the hard ~20% (multi-day de-novo assembly) and is intentionally skipped.
- BUSCO completeness ("7 fragmented, 5 missing of 1,658", insecta_odb9): in principle reproducible but BUSCO v3/odb9 era; exact frag/missing counts are fragile across BUSCO/AUGUSTUS versions. Treated as optional stretch, not core.
- Venom-peptide gene annotation, tandem organization, phylogenetics, expression: manual/specialized annotation + wet-lab — out of scope.
Compute
All on «our HPC» («infra» workdir), per HARD RULES. FASTA fetched inside the compute
job from ENA; assemblathon_stats.pl cloned on «infra»; only the small text
stats report is pulled back to «host».
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.
All four checked genome-assembly statistics (total size 258 Mb, scaffold N50 22.4 Mb, L50 5, 11 chromosomes) reproduce exactly from the authors' deposited assembly GCA_928718305.1 using the brief's own tool, with deviations only at the rounding level. The values are fully derivable from public data and there is no fabrication concern. The one caveat is methodological, not a defect: this is a consistency check on the deposited final FASTA (the un-deposited MaSuRCA intermediate and the venom-peptide phylogenetics were out of scope), but every claim actually tested holds 1:1.
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.