Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes

Whole-genome duplication (WGD) has been proposed as a catalyst for evolutionary innovation in seed plants and angiosperms, yet its 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 put..., , # Data from: Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes

Dryad DOI: https://doi.org/10.5061/dryad.gb5mkkx3z

This repository is associated with Shi, T. & Van de Peer, Y. (2025). Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes. Science Advances. In Press.

In this study, Ortholog Groups (OGs) are clustered by Orthofinder2 based on plants listed in Table S1 of our current manuscript (Shi & Van de Peer, 2025). The gene trees from OGs were based on FastTree v2, which were used for reconciliation with the species tree using Notung v2.9. In this reconciliation process, we applied a tree rearrangement threshold of 0.9 based on the SH-like score (tree node support) to minimize the duplication/loss cost.

This repository contains the scripts, OG files, and gene tree files necessary to perform dosage-sensitivity assessment of each OG by correlati...,