Extensive variation between chromosomes of North American and European hop.
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. Fresh REAL compute on «our HPC» (the prior 2026-06-21 run's «infra» work dir had been reclaimed by the janitor, so everything was re-downloaded and re-run from scratch; results are identical, confirming reproducibility). Third-party tools applied to the paper's own deposited data per brief P16. C1 HiFi yield: seqkit-streamed 119.94 Gb across the 5 main HiFi cells (~120 Gb), every run matching ENA base_count, coverage 24.4x (exact, «job»). C2: exactly 10 chromosome pseudomolecules incl. X (exact). C3: chromosome span 2.62 Gb vs ~2.5 Gb (within-tol; paper itself flags span > expected). C4: chromosome N50 272.4 Mb confirms chromosome-scale (partial - paper's exact N50 not in accessible text). C5 FLAGSHIP: BUSCO v5.8.2 embryophyta_odb10 genome mode = 98.0% complete, matching reported ~98% (exact, «job»). IMPORTANT: harvested code/data pointers are text-mining MISPAIRS - code 'PacificBiosciences/ccs' is the HiFi consensus tool (only consensus reads deposited, so not re-runnable) and data 'PRJNA906612' is Illumina RAD-Seq, NOT the assembly data; the real Apollo deposits are ENA PRJEB63995 (reads) + GCA_963992765 (haploid assembly) + GCA_964017075 (diploid 4.92 Gb). NOT attempted (heavy/parameter-sensitive 20%): de-novo assembly, annotation, inter-haplotype SVs, population genomics, GWAS, metabolomics. No fabrication signal: all reproduced values are real-compute-derivable, mutually self-consistent, and the assembly fasta.gz sha256 (6b6eb4ce...) is stable across both independent runs.
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 87assessed: 2026-06-21 ⛓ 7576cb7d1905
✎ 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
- 2026-06-24
- 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: sonnetHow European and North American hop ancestries contribute to bitter acid content, the most important trait in hop breeding, given that most modern hop cultivars are Eu-NAm hybrids but the genomic structure and impact of this interspecific breeding has remained unclear.
- ★ Chromosome-scale, haplotype-resolved genome assemblies of the hybrid hop cultivar Apollo were generated using hifiasm, ALLHiC, and TRITEX pipelines with PacBio HiFi and Hi-C data method
- ★ European (Eu) and North American (NAm) ancestry was assigned across the Apollo genome using species-specific high-copy k-mer markers derived from repetitive regions method
- ★ Varying levels of recombination suppression exist between chromosomes of Eu and NAm origin in interspecific Humulus hybrids finding
- ★ Genetic and chemical diversity exists in core bittering pathways between European and North American hops finding
- ★ Beneficial Eu and NAm alleles show additive effects on bitter acid (α-acid) content finding
- Homologous chromosome pairs with contrasting Eu/NAm origin show substantial sequence divergence (~75-78% identity), while same-origin pairs are nearly identical (>98.5%) finding
- Meiotic abnormalities and non-Mendelian segregation occur in hop generally, not only in Eu-NAm hybrids, suggesting divergent ancestry is not the sole cause of suppressed recombination finding
- ★ Apollo genome shows biased chromosome retention with phase 1 predominantly NAm and phase 2 predominantly Eu origin, contrasting the expected intermixed mosaic pattern of multi-generation hybrids finding
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| PacBio HiFi (CCS) long-read sequencing + Hi-C scaffolding | hop cv. Apollo (Eu-NAm hybrid) | none | chromosome-scale phased diploid genome assembly | hifiasm, ALLHiC, TRITEX pipelines |
| BUSCO completeness analysis | hop cv. Apollo phased genome assembly | none | assembly completeness (% complete orthologs) | BUSCO |
| Fluorescence in situ hybridization (FISH) cytogenetics on mitotic metaphase chromosomes | hop cv. Apollo | none | localization of HSR subtelomeric repeat and 45S rDNA, karyotype | DAPI counterstaining/microscopy |
| Genotyping-by-sequencing (GBS) | feral and wild European and North American Humulus genotypes | none | mapping to Apollo assembly to validate Eu/NAm ancestry assignment | — |
| Linkage mapping (pseudo-test cross strategy) | three biparental mapping populations: Apollo × PubM_740, Zenith × USDA21058M, Cascade × HL-19-060-002M | Eu-NAm hybrid cross vs H. lupulus cross | recombination rate, genetic map distance (cM), marker segregation | — |
| GBS genotyping | 243 accessions (breeding lines, H. lupuloides, H. neomexicanus, commercial cultivars, H. lupulus) | none | proportion/preference of Eu-NAm chromosome pair combinations | — |
| K-mer analysis of repetitive DNA families | hop cv. Apollo genome | none | identification of species-specific (Eu vs NAm) high-copy k-mer markers | — |
| Genome-wide diversity/divergence analysis (nucleotide diversity π, dXY) | hop cv. Apollo haplotypes | none | correlation of sequence divergence with recombination suppression across chromosome arms | — |
- – Diploid Apollo genome assembled from 120 Gb CCS reads (~24-fold coverage) with ~98% complete BUSCO orthologs in both phases 24-fold coverage; ~98% BUSCO complete
- ▼ Phase switch error analysis showed only a small fraction of SNPs indicating phase switches, confirming proper haplotype phasing 2.085% (122,753/5,886,045 SNPs)
- – Homologous pseudomolecules with contrasting Eu/NAm assignment show substantial divergence, while same-origin pairs are nearly identical ~75-78% identity (Eu-NAm) vs >98.5% (same origin)
- ▼ No or strongly suppressed recombination detected in Apollo × PubM_740 and Zenith × USDA21058M populations; no linkage maps could be constructed
- – Cascade × HL-19-060-002M population produced a normal genetic map with no evidence of suppressed recombination 2864.69 cM, 8751 markers, 4.23 markers/cM, 1-2 breakpoints/chromosome
- – Apollo genome shows biased retention of parental haplotypes (phase 1 mostly NAm, phase 2 mostly Eu) rather than the expected intermixed mosaic from multiple hybrid generations
- – Eu and NAm lineage haplotypes estimated to have diverged approximately 1.05 million years ago ~1.05 Mya
- ▼ Cited cytological data show fewer than 5% of diakinesis-stage nuclei exhibit the expected ten bivalents from correct chromosome pairing <5%
- pvalue_or_ratio 2.085% (122,753/5,886,045 SNPs) phase switch error (phasing accuracy of Apollo assembly)
- other ~75-78% median sequence identity (Eu vs NAm homologous chromosome pairs)
- other >98.5% sequence identity (same-origin (NAm-NAm or Eu-Eu) chromosome pairs)
- count 2864.69 cM genetic map, 8751 markers, 4.23 markers/cM (Cascade × HL-19-060-002M linkage map)
- other 24-fold coverage from 120 Gb CCS reads (Apollo diploid genome sequencing depth)
- other ~98% complete BUSCO orthologs (assembly completeness, both phases)
- other <5% of diakinesis nuclei with 10 bivalents (cited meiotic pairing study (Zhang et al.))
- other ~1.05 Mya divergence estimate (Eu-NAm haplotype divergence time)
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 chromosome-scale, haplotype-resolved diploid genome assembly of hop cultivar Apollo from ~120 Gb CCS long reads (24× diploid coverage) processed through hifiasm, ALLHiC, and TRITEX pipelines with Hi-C scaffolding. European and North American ancestral haplotypes were assigned genome-wide via a k-mer frequency approach leveraging species-specific repetitive elements. Recombination between ancestral chromosomes was evaluated through pseudo-testcross linkage mapping in three bi-parental populations, and population genetic diversity was characterised using nucleotide diversity (π) and haplotype divergence (dXY) from GBS data on 243 accessions. Results are reported primarily as descriptive metrics (percentages, sequence identities, map lengths) without classical frequentist inference in the text excerpt provided; the abstract notes additive effects of beneficial alleles on α-acid content but those analyses are not yet visible in the provided text.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Pseudo-testcross linkage mapping (markers heterozygous in hybrid parent, expected 1:1 segregation) | Recombination assessment across all ten chromosomes in three bi-parental populations (Apollo × PubM_740; Zenith × USDA21058M; Cascade × HL-19-060-002M) | 8751 markers heterozygous in Cascade for the Cascade × HL-19-060-002M population; n not stated for the other two populations | not stated |
| BUSCO completeness scoring | Assembly quality evaluation of both phases of the phased Apollo assembly | null | na |
| SNP-based phase switch error estimation | Haplotype phase quality assessment across all SNPs in the phased assembly | 5886045 SNPs assessed | not stated |
| K-mer frequency analysis for haplotype-of-origin assignment | Partitioning of Eu and NAm haplotypes in phased Apollo assembly using differentially enriched high-copy k-mers | null | not stated |
| Nucleotide diversity (π) and haplotype divergence (dXY) estimation | Genome-wide population genetic characterisation; tested for correlation with recombination suppression across chromosome arms | 243 accessions genotyped by GBS | not stated |
| Pairwise whole-genome sequence identity comparison | Divergence between Eu and NAm haplotype pairs (~median 75–78%) vs. same-lineage pairs (>98.5%) | null | not stated |
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Deviation from Mendelian 1:1 segregation in mapping populations was noted qualitatively (linkage maps could not be generated in two of three populations); no formal test of segregation distortion was described↳ Could also: Chi-square goodness-of-fit or exact binomial tests per marker locus, with Benjamini–Hochberg FDR correction applied across the marker panel — Formal per-locus testing would provide genome-wide significance maps of segregation distortion, enabling quantitative distinction between loci with mild distortion and those with near-complete recombination suppression, and would make the findings directly comparable with published distortion surveys in other species
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Eu/NAm haplotype origin was assigned using a k-mer approach derived from within the Apollo assembly, without separate parental reference genomes↳ Could also: Trio-binning using sequenced parental genomes (explicitly discussed in the paper as an established alternative for F1 hybrids with known parents) — When parental sequences are available, trio-binning provides an independent, orthogonal validation of haplotype-of-origin assignments; the within-assembly k-mer approach used here extends applicability to advanced-generation hybrids where parental genomes are unavailable, which is the scenario the paper addresses
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The absence of a consistent correlation between recombination suppression and local sequence divergence (π, dXY) was inferred from visual inspection of Supplementary Fig. 13 without a quantitative test↳ Could also: Spearman rank correlation with permutation-based (label-shuffling) significance assessment between windowed recombination rate estimates and windowed π or dXY along each chromosome arm — A formal correlation test with an explicit significance threshold would provide a quantitative measure of association and its uncertainty, which could strengthen or qualify the conclusion that sequence divergence does not drive local recombination suppression
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Assembly completeness was assessed with BUSCO (~98% in both phases)↳ Could also: Complementary k-mer-based quality value (QV) estimation (e.g., via Merqury) and long-terminal-repeat assembly index (LAI) scoring — BUSCO captures single-copy gene completeness but does not assess base-level accuracy or the continuity of repetitive regions, which comprise the majority of the hop genome; QV and LAI provide complementary metrics that are increasingly expected in plant reference genome reports and together give a more complete picture of assembly quality
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Genetic map statistics (total length, marker density) were reported as point estimates for the Cascade × HL-19-060-002M population without accompanying uncertainty estimates↳ Could also: Bootstrap resampling of progeny individuals to obtain confidence intervals on total map length and per-chromosome recombination rate — Bootstrap CIs on map statistics would quantify sampling uncertainty, which is particularly informative when contrasting populations with very different apparent recombination rates and when progeny sizes affecting marker-order precision are not reported
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The 243 GBS-genotyped accessions were classified into predefined categories (breeding lines, H. lupuloides, H. neomexicanus, commercial cultivars, H. lupulus)↳ Could also: Model-based admixture analysis (e.g., ADMIXTURE or fastSTRUCTURE) or principal component analysis of genome-wide SNPs — These approaches provide continuous, per-individual estimates of Eu/NAm ancestry proportions independently of predefined taxonomic labels, and could reveal fine-scale population structure or intermediate admixture levels not captured by the binary ancestry classification used
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-42204144
Paper: Extensive variation between chromosomes of North American and European hop. Nat Commun (2026). PMID 42204144 · PMCID PMC13216280 · DOI 10.1038/s41467-026-72379-8. Subject: haplotype-resolved phased genome assembly of the NAm×Eu hybrid hop cultivar 'Apollo' (Humulus lupulus), plus variation/population genomics.
Important correction to the harvested metadata
The room was seeded with code = github.com/PacificBiosciences/ccs and
data = sra:PRJNA906612. Both are text-mining mispairs for this paper:
- PRJNA906612 is 272 Illumina RAD-Seq runs (single-end NovaSeq 6000, ~177 Gbp; verified via ENA portal API). It is not this paper's primary deposit and contains no PacBio data. This paper's data are deposited at ENA under PRJEB... accessions (see below). PRJNA906612 is a previously-published RAD-Seq population set referenced in the literature, not the Apollo data.
- PacificBiosciences/ccs is the PacBio HiFi read-generation tool. The paper
used CCS reads, but its only deposited code is a metabolomics repo
(
carlsberglaboratorium-publications/apollo-cone-development-metabolomics, Zenodo 10.5281/zenodo.19134880) — unrelated to the genomics pipeline. The genomics pipelines (hifiasm, ALLHiC, TRITEX, RagTag, MUMmer, BUSCO) are published third-party tools applied with cited parameters; no custom code was deposited. Per the brief (P16), applying an existing third-party tool to the paper's own data is an equally valid reproduction — that is what we do.
The raw PacBio subreads are not deposited (only the already-consensus CCS/HiFi
reads at PRJEB63995), so ccs itself cannot be re-run; it is moot for
reproduction. We instead reproduce deterministic pipeline outputs on the paper's
own deposited assembly + reads.
This paper's real deposits (ENA, verified)
- PRJEB63995 — CCS (HiFi), RNA-Seq, Iso-Seq, Hi-C reads for the Apollo assembly.
- PRJEB64169 — contigs + AGP of the haploid Apollo assembly → registered assembly GCA_963992765 (Apollo_haploid, chromosome-level).
- PRJNA1082089 / PRJEB64593 — phased (2-haplotype) assembly; scaffold-level combined assembly registered as GCA_964017075 (Apollo_nrgene, 4.92 Gb).
In scope (pipeline-derived, clearly specified, low-hanging — attempted)
| # | Reported result | Pipeline / tool | Reproduction approach |
|---|---|---|---|
| C1 | "120 Gb CCS reads, 24-fold coverage of the diploid genome" | PacBio CCS (the named tool's output) | Sum base_count of deposited HiFi runs at PRJEB63995 (control-plane ENA query) |
| C2 | Haploid assembly = 10 pseudomolecules incl. X, named per Cannabis cs10 | hifiasm→ALLHiC→TRITEX | Count chromosome-scale sequences in deposited GCA_963992765 |
| C3 | Haploid genome size ~2.5 Gb | (assembly) | seqkit total length on GCA_963992765 |
| C4 | Assembly contiguity / scaffold N50 | (assembly) | seqkit N50 on GCA_963992765 |
| C5 | "~98% complete BUSCO" (assembly completeness, embryophyta_odb10) | BUSCO v5 (third-party tool) | BUSCO v5.7.1 embryophyta_odb10 genome mode on GCA_963992765 («our HPC») |
Out of scope (heavy last-20% or non-pipeline — not attempted, with reason)
- Full de novo assembly (hifiasm+ALLHiC+TRITEX on 120 Gb HiFi + Hi-C, 5 Gb diploid genome): multi-day, multi-TB; the heavy ~80%. We instead validate the deposited assembly's reported metrics. Not attempted by design (80/20).
- Gene annotation (30,920 / 30,398 HC gene models): bespoke EVM/Mikado pipeline, RNA/Iso-Seq evidence, no deposited code → not reproducible at 80/20.
- Phase-switch SNPs (122,753 / 5,886,045) and SVs (52,593 PAV / 41,990 TRANS / 4,438 INV): MUMmer/RagTag between phases — tractable but the harder 20%; deferred unless C1–C5 leave budget.
- Population genomics (33,178 SNPs over 243 genotypes), GWAS, linkage maps, metabolomics, phylogenetics: parameter-sensitive RAD/GBS pipelines and wet-lab/chemistry
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. Working from the authors' own deposited reads (ENA PRJEB63995) and assembly (GCA_963992765), real SLURM compute reproduced HiFi yield (119.94 Gb ≈ 120 Gb, 24.4x), the 10 pseudomolecules including X, and BUSCO completeness (98.0% vs ~98%) exactly, with chromosome span 2.62 Gb within +4.9% of the reported ~2.5 Gb — a deviation the paper itself flags. The only gap is C4's exact tabulated N50 (Suppl. Table 4 not in fetched text), but the measured 272.4 Mb N50 confirms the qualitative chromosome-scale claim. No fabrication signal: all values are real-compute-derivable and mutually self-consistent. Worth documenting for cross-study stats: the manifest's harvested code/data pointers are text-mining mispairs (CCS tool repo and a RAD-Seq project), not the actual deposits — a metadata-harvesting anomaly, not an authors' or reproduction defect.
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.