G4 Paradox v2 Reproducibility Package: Compartment-dependent selection regimes maintain the G-quadruplex paradox across the eukaryotic kingdoms
Authors: tanigawa, masato, Iwaki, Takafumi
Type: Dataset
Published: 2026-08-03
Keywords: G-quadruplex, comparative genomics, eukaryotic evolution, two-regime architecture

<p>Reproducibility package for the v2 manuscript analysing the<br>G-quadruplex (G4) paradox across 198 reference genomes spanning the<br>four eukaryotic kingdoms (Animalia n=86, Fungi n=49, Plantae n=33<br>including the gymnosperm Ginkgo biloba, Protozoa n=30).</p>
<p>Includes: 43 analysis scripts in total (29 main + 4 upstream<br>G4-detection/dG-stability/feature-compile + 10 experimental-<br>validation for BG4 ChIP-seq, G4P-ChIP and rG4-seq overlap; Python<br>3.9 + bash), curated sample metadata (species_features_v2.tsv,<br>species trees, NCBI/Ensembl/WormBase/Ginkgo accessions), full<br>analytical outputs (helicase counts, PGLS results on curated and<br>Open Tree of Life synthetic trees, polytomy-free 146-species<br>sensitivity, per-pair CAI control for 7 unsaturated dN/dS pairs,<br>Nei-Gojobori dN/dS for 9 pairs with parametric 95% CI, motif age<br>stratification, BG4/G4P/rG4-seq overlap statistics), and the<br>complete Supplementary Information PDF plus six supplementary<br>tables S1-S6 (TSV).</p>
<p>Key findings reproducible from this deposit:</p>
<p>(i) Cross-kingdom architecture. CDS depletion and intergenic<br>enrichment of stable G4 motifs are strictly sign-consistent across<br>all four sampled eukaryotic kingdoms under an aggregation rule that<br>requires all four kingdom medians to be non-zero and share the same<br>sign (Rule B; joint binomial P = 0.049). Intronic and promoter<br>enrichment additionally become sign-concordant under a<br>tie-permissive rule that treats a kingdom median of exactly zero<br>as compatible with same-signed non-zero medians (Rule A; joint<br>P = 2 x 10^-4), yielding a four-region cross-kingdom architecture.<br>The tie kingdoms are Protozoa intron (15/30 species with zero stable<br>intronic G4) and Fungi promoter. See CORRECTION_NOTES.md.</p>
<p>(ii) Two-regime selection architecture (central synthesis).<br>In coding sequence, codon-adaptation selection takes priority: a<br>naive Nei-Gojobori comparison reproduces 5-16% dS suppression at<br>G4-overlapping codons in 6/7 unsaturated species pairs, but the<br>signal is fully absorbed by per-gene CAI adjustment (0/7 pairs<br>retain a G4 odds ratio significantly below 1; 5/7 reverse to<br>OR > 1). In introns and promoters, selection acts directly on G4<br>structure: PGLS yields five Benjamini-Hochberg-significant<br>kingdom-specific helicase associations at q < 0.10, all at intronic<br>or promoter G4s, including context-dependent FANCJ/BRIP1 (positively<br>with intron G4 in Plantae, beta = +1.54, q = 0.057; negatively with<br>promoter G4 in Protozoa, beta = -2.49, q = 0.004); three of the<br>five remain BH-significant on the independent Open Tree of Life<br>backbone.</p>
<p>(iii) Intronic G4 are concentrated in deeply conserved gene<br>families (root- or LECA-level orthologue groups in >= 87.5% of<br>cases across all four kingdoms), consistent with the host-gene<br>context of intronic G4 having been broadly maintained since early<br>eukaryotic evolution.</p>
<p>The published figures (Figure 1 G4 paradox overview, Figure 2<br>sample composition, Figure 3 naive dN/dS, Figure 4 PGLS forest,<br>Figure 5 motif age) and the manuscript itself are not included in<br>this deposit (subject to publishing journal copyright); figures<br>are regenerable from the deposited data using the included<br>plotting scripts.</p>
<p>Companion paper: Tanigawa & Iwaki (2026) "G4-quadruplex analysis<br>of coronaviruses reveals functional constraints and antiviral<br>therapeutic opportunities", Virus Research 364:199692,<br>DOI: 10.1016/j.virusres.2026.199692.</p>
<p>In accordance with the CSHL Press policy on AI tools, Anthropic's<br>Claude (model: claude-opus-4-7, 1M-context configuration; accessed<br>via the Claude Code CLI in agentic-coding mode between 2026-04-15<br>and 2026-07-14) was used for script drafting, language editing,<br>and post-submission reproducibility audit under explicit<br>version-controlled human review. The AI assistant did not generate<br>research data, run statistical analyses autonomously, propose<br>scientific interpretations independently, or produce figure<br>content. All analytical decisions, code, computed values, figures,<br>interpretations, and conclusions were independently verified by the<br>authors, who take full responsibility for the accuracy and<br>integrity of this deposit.</p>
<p><br>## Version 2 (2026-07-14): Post-submission corrections</p>
<p>This version contains three post-submission corrections to the<br>initial deposit, disclosed to the Genome Research editorial office<br>on 2026-07-14. See CORRECTION_NOTES.md at the root of the deposit<br>for the full change log. Summary:</p>
<p>1. Table 1 of the manuscript body: Fungi and Protozoa intron<br>   medians corrected against the deposited species_features_v2.tsv.<br>2. Sign-consistency test: aggregation rule made explicit; two<br>   rules (strict Rule B and tie-permissive Rule A) reported.<br>3. PIF1 KEGG identifier: Methods corrected from K11385 (which<br>   returns zero copies) to K15255 (the operative identifier used<br>   in the analysis).</p>
<p>The central two-regime architecture finding is unchanged.</p>
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<p>## Version 7 (2026-08-03): Interim documentation correction</p>
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<p>This version accompanies bioRxiv v3 update and applies documentation-<br>level corrections identified in a coauthor audit (attached at<br>deposit root as AUDIT_REPORT.md). Central analytical claims of the<br>main manuscript remain under clean-environment re-verification;<br>readers are advised to consult AUDIT_REPORT.md and the manuscript's<br>Interim-correction notice (page 2) for the current list of open<br>methodology-level issues. This is an interim documentation<br>correction, not a fully verified revision.</p>
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