DOI: 10.5061/dryad.gb5mkkx3z
title: Data from: Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes

description: 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 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.
description: # 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 correlation between observed and expected OG copy numbers,
 gene-tree, and species-tree reconcilation for phylogenetic placement of
 Amborella & Aristolochia gene duplication events. The software
 included in these scripts is: R, Notung, Perl, and WGDgc. All software is
 open source and free to access. #### Files and variables File: data.zip
 Description: 'data.zip' (after uncompressing) contains 1) folder
 'OG_nonseedPlants' with ortholog groups (OGs) list related to
 Fig. 4 of the manuscript, 2) folder 'geneTrees_LandPlants' with
 gene tree files of .nwk format related to Fig. 5 of the manuscript, 3)
 folder 'OG_LandPlants' contains ortholog groups (OGs) related to
 Fig. 5, 4) folder 'OG_LandPlantsSmall' contains ortholog groups
 (OGs) related to Fig. 6 ## Code/software File: codes.zip
 Description:codes.zip contains codes for WGD detection, including 1)
 'WGDdetection.txt' contains code for Dosage sensitivity
 assessment for OGs, and WGD detections using gene-tree-and-species-tree
 reconcilation, and WGDgc, 2) 'z_all_childnodes1.pl' and
 'z_bulk_childnodes.pl' are Perl scripts used
 in'WGDdetection.txt' ## Access information Other publicly
 accessible locations of the data: N/A Data was derived from the following
 sources: N/A