G4 Paradox v2 Reproducibility Package: Compartment-dependent selection regimes maintain the G-quadruplex paradox across the eukaryotic kingdoms

Reproducibility package for the v2 manuscript analysing theG-quadruplex (G4) paradox across 198 reference genomes spanning thefour eukaryotic kingdoms (Animalia n=86, Fungi n=49, Plantae n=33including the gymnosperm Ginkgo biloba, Protozoa n=30). Includes: 43 analysis scripts in total (29 main + 4 upstreamG4-detection/dG-stability/feature-compile + 10 experimental-validation for BG4 ChIP-seq, G4P-ChIP and rG4-seq overlap; Python3.9 + bash), curated sample metadata (species_features_v2.tsv,species trees, NCBI/Ensembl/WormBase/Ginkgo accessions), fullanalytical outputs (helicase counts, PGLS results on curated andOpen Tree of Life synthetic trees, polytomy-free 146-speciessensitivity, per-pair CAI control for 7 unsaturated dN/dS pairs,Nei-Gojobori dN/dS for 9 pairs with parametric 95% CI, motif agestratification, BG4/G4P/rG4-seq overlap statistics), and thecomplete Supplementary Information PDF plus six supplementarytables S1-S6 (TSV). Key findings reproducible from this deposit: (i) Cross-kingdom architecture: CDS depletion and intronic /promoter enrichment of stable G4 motifs are sign-consistent acrossall four sampled eukaryotic kingdoms. (ii) Two-regime selection architecture (central synthesis).In coding sequence, codon-adaptation selection takes priority: anaive Nei-Gojobori comparison reproduces 5-16% dS suppression atG4-overlapping codons in 6/7 unsaturated species pairs, but thesignal is fully absorbed by per-gene CAI adjustment (0/7 pairsretain a G4 odds ratio significantly below 1; 5/7 reverse toOR > 1). In introns and promoters, selection acts directly on G4structure: PGLS yields five Benjamini-Hochberg-significantkingdom-specific helicase associations at q < 0.10, all at intronicor promoter G4s, including context-dependent FANCJ/BRIP1 (positivelywith intron G4 in Plantae, beta = +1.54, q = 0.057; negatively withpromoter G4 in Protozoa, beta = -2.49, q = 0.004); three of thefive remain BH-significant on the independent Open Tree of Lifebackbone. (iii) Intronic G4 are concentrated in deeply conserved genefamilies (root- or LECA-level orthologue groups in >= 87.5% ofcases across all four kingdoms), consistent with the host-genecontext of intronic G4 having been broadly maintained since earlyeukaryotic evolution. The published figures (Figure 1 G4 paradox overview, Figure 2sample composition, Figure 3 naive dN/dS, Figure 4 PGLS forest,Figure 5 motif age) and the manuscript itself are not included inthis deposit (subject to publishing journal copyright); figuresare regenerable from the deposited data using the includedplotting scripts. Companion paper: Tanigawa & Iwaki (2026) "G4-quadruplex analysisof coronaviruses reveals functional constraints and antiviraltherapeutic opportunities", Virus Research 364:199692,DOI: 10.1016/j.virusres.2026.199692. In accordance with the CSHL Press policy on AI tools, Anthropic'sClaude (model: claude-opus-4-7, 1M-context configuration; accessedvia the Claude Code CLI in agentic-coding mode between 2026-04-15and 2026-05-22) was used for script drafting and language editingunder explicit version-controlled human review. The AI assistantdid not generate research data, run statistical analysesautonomously, propose scientific interpretations independently, orproduce figure content. All analytical decisions, code, computedvalues, figures, interpretations, and conclusions wereindependently verified by the authors, who take full responsibilityfor the accuracy and integrity of this deposit.