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Cyclin Ortholog Retention Across Brassica Allotetraploids by Subgenome — Real Data

The most complete published dataset for this question comes from a genome-wide survey of 1,087 cyclin genes across ten Brassicaceae genomes (six Brassica species of U's triangle plus four Arabidopsis species), which used 49 curated Arabidopsis thaliana cyclins as queries, Pfam domain validation, and reciprocal BLASTp, then OrthoFinder to assign one-to-one orthologs between each diploid progenitor and its allotetraploid derivative, with retention defined as an ortholog located on the expected subgenome (e.g., B. rapa genes on the A subgenome) and "exchange" defined as an ortholog found on a non-expected subgenome Brassica cyclin genome-wide evolution study.

Gene-Count Bar Chart Data: Cyclin Copy Number per Species (Diploid Reference vs. Allotetraploid)

The diploid progenitor reference counts and allotetraploid totals needed for a paired bar chart ("retention capacity" — what the allotetraploid starts with before fractionation) are published:

*76 is the independent B. rapa genome-wide count using BrassicaDB annotation with 10 Arabidopsis cyclin queries; ~90 is from the 10-species comparative framework (diploid average 71.5, range 90–189 across all six Brassica) — the discrepancy reflects differing annotation sets and query panels B. rapa 76-cyclin genome-wide studySpecies cyclin totals and duplication events.

Within B. napus, a CYCB-specific study found 25 CYCB genes in the Darmor-bzh reference (11 on the A subgenome, 13 on the C subgenome, 1 on a scaffold), expanding to 299 CYCB genes across 11 accessions (20–30 typical, up to 50 in Ningyou) — showing accession-level copy-number variation on top of the fixed subgenome-level retention B. napus CYCB subgenome split A:11/C:13. The near-even 11:13 A:C CYCB split is consistent with the balanced (~2:2) expectation from subgenome-wide fractionation analyses where multi-copy genes show ~40% per subgenome and no strong subgenome bias WGD-triplication and dosage-balance context.

All values from the published ortholog-retention analysis (Table S9 summarized in main text); retention ranged 66.6–87.5% and exchange 12.5–33.3% across the six progenitor–allotetraploid combinations Subgenome retention percentages table.

A key asymmetry: the B genome in B. juncea shows the highest retention (87.5%), while the same B. nigra progenitor shows the lowest retention in B. carinata (66.6%) — retention is not an intrinsic property of the progenitor genome but depends on the recipient allotetraploid background, consistent with extensive homoeologous exchange and genome reshuffling in allopolyploid Brassica Exchange vs retention asymmetry.

Ready-to-Render Chart Specifications (from the real published numbers)

combinations = {
 "B.rapa→B.napus (A)": 67.7, "B.oleracea→B.napus (C)": 68.8,
 "B.rapa→B.juncea (A)": 73.9, "B.nigra→B.juncea (B)": 87.5,
 "B.nigra→B.carinata (B)": 66.6, "B.oleracea→B.carinata (C)": 70.4}
exchanged = {"A":32.2,"C":31.2,"A":26.0,"B":12.5,"B":33.3,"C":29.5}

Per-cyclin-type ortholog data for a heatmap (ortholog pairs, progenitor genes involved): cycT1 (83 pairs, 38 genes), cycA2 (81, 36), cycB2 (76, 34), cycB1 (69, 32), cycD3 (64, 28), cycU4 (61, 24), cycA3 (55, 24), cycA1 (48, 19); among D-types, cycD3 retained the most pairs (64) while cycD5 was lowest (14) Per-cyclin-type ortholog pair counts. Duplication-mode breakdown for a proportional bar chart: of 1,845 total duplication events, 969 were WGD, 730 dispersed, 75 transposed, 51 tandem, 20 proximal; intra- vs inter-genomic splits in allotetraploids were B. napus 149 intra (83 A + 66 C) vs 214 inter; B. juncea 147 intra vs 212 inter; B. carinata 120 intra vs 154 inter Duplication-mode breakdown data.

Summary: What the Graphs Show

For flowering-time relevance in B. napus: two cyclins (Bna21cycA2, Bna113cycD4) co-localize with flowering-time QTL and carry diagnostic amino-acid polymorphisms in early-flowering cultivars (Westar, No2127) — a candidate downstream application of the retention data Cyclin flowering-time QTL candidates.

Explore B. napus cyclin subgenome data → Explore B. juncea / B. carinata retention → Explore B. rapa cyclin family →

Limitations and epistemic caveats

• Retention percentages are computed on one-to-one OrthoFinder pairs against a 49-gene A. thaliana reference — not all cyclin genes in each genome enter the denominator; one-to-many relationships are excluded, so these figures measure subgenome placement of orthologous copies, not total gene survival.
• The three species-level totals come from a single 2026 framework using specific annotation sets; counts differ across studies (e.g., 76 vs ~90 for B. rapa) because of differing query panels and annotation versions, so cross-study totals should not be mixed in one chart.
• "Exchange" here means an ortholog sits on a non-expected subgenome — evidence of homoeologous exchange rather than of new independent origins; the causal contribution of homoeolog exchange vs. ancestral fractionation to each case is not fully resolved.
• B. juncea's highest duplication frequency (377 events, 68% WGD) co-occurs with its highest B-subgenome retention, but no direct causal test of this association exists.