Abstract
Whole-genome duplication (WGD) has been proposed as a catalyst for evolutionary innovation in seed plants and angiosperms, yet their occurrence remains contentious. By integrating gene dosage balance principles with phylogenomic reconciliation and probabilistic modeling, we revisit the debated ancestral seed and angiosperm WGDs. Leveraging dosage-sensitive orthologous gene groups (OGs) as evolutionary markers across representative plants for gene tree/species tree reconciliation, we demonstrate that gene retention patterns in Amborella and Aristolochia —early-diverging plants lacking post–angiosperm origin WGDs—reveal a single gene duplication peak predating the seed plant diversification, with no signal of ancestral angiosperm WGD. Correlation analyses of observed and expected OG copy numbers, given proposed WGD(s), further refute an angiosperm WGD. Probabilistic retention modeling analysis corroborates these findings and shows that retention rates of dosage-sensitive genes from the putative angiosperm WGD are extremely low. Besides, our study establishes that genes inferred to have higher dosage sensitivity based on their sequential retention following WGD events may have increased utility in resolving ancestral polyploidy.
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Claims 5
Claim · model-written summary
Gene retention in Amborella and Aristolochia reveals a single gene duplication peak predating seed plant diversification.
- Taxon
- Amborella and Aristolochia
Aristolochia_fragment.jpg?width=60)
Amborellae1 - Outcome
- a single gene duplication peake1
- Qualifier
- predating the seed plant diversificatione1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
_fragment.jpg?width=500)
Verbatim
e1“gene retention patterns in Amborella and Aristolochia —early-diverging plants lacking post–angiosperm origin WGDs—reveal a single gene duplication peak predating the seed plant diversification, with no signal of ancestral angiosperm WGD”
Claim · model-written summary
Gene retention in Amborella and Aristolochia shows no signal of an ancestral angiosperm WGD.
- Taxon
- Amborella and AristolochiaAristolochiaAmborellae1
- Outcome
- signal of ancestral angiosperm WGDe1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“gene retention patterns in Amborella and Aristolochia —early-diverging plants lacking post–angiosperm origin WGDs—reveal a single gene duplication peak predating the seed plant diversification, with no signal of ancestral angiosperm WGD”
Claim · model-written summary
Correlation analyses of observed and expected OG copy numbers further refute an angiosperm WGD.
Verbatim
e0“as evolutionary markers across representative plants”
e3“Correlation analyses of observed and expected OG copy numbers, given proposed WGD(s), further refute an angiosperm WGD”
Claim · model-written summary
Retention rates of dosage-sensitive genes from the putative angiosperm WGD are extremely low.
Verbatim
e0“as evolutionary markers across representative plants”
e4“retention rates of dosage-sensitive genes from the putative angiosperm WGD are extremely low”
Claim · model-written summary
Genes with higher dosage sensitivity from sequential retention may be useful for resolving ancestral polyploidy.
Verbatim
e0“as evolutionary markers across representative plants”
e5“genes inferred to have higher dosage sensitivity based on their sequential retention following WGD events may have increased utility in resolving ancestral polyploidy”