Data for: Phylogenomic Profiles of Whole-Genome Duplications in Poaceae and Landscape of Differential Duplicate Retention and Losses among Major Poaceae Lineages

Here, we present sequence alignments and gene tree files of orthogroups and their reconciliations as described in our publication titled “Phylogenomic Profiles of Whole-Genome Duplications in Poaceae and Landscape of Differential Duplicate Retention and Losses among Major Poaceae Lineages”.The ‘Grass Phylogenomics’ folder includes datasets for estimation of retention/loss patterns of the rho-derived duplicates, which were used for our custom scripts in GitHub and the online tool in Code Ocean (10.24433/CO.1170454.v1).The “Bayesian divergence time estimation” folder consists of datasets for dating Poaceae time-tree. The folder of Alignments includes nuclear gene alignments of 166 single-copy gene families. The DatedTrees folder comprises 166 dated trees. Grass.time.tree is the dated tree summarized from 166 dated trees and corresponds to our Supplementary Figure 2.Datasets for phylogenomic analyses using Tree2GD, corresponding to our Supplementary Figures 3-16, are available in folders of “Phylogenomic analyses for Poaceae and other Poales”, “Phylogenomic analyses for Poaceae”, “Phylogenomic analysis for Bambusoideae”, “Phylogenomic analyses for Oryzoideae”, “Phylogenomic analyses for Pooideae”, “Phylogenomic analyses for Poeae”, “Phylogenomic analyses for Agrostidodinae and Poodinae”, “Phylogenomic analyses for Triticodae”, “Phylogenomic analysis for Panicoideae”, “Phylogenomic analyses for Panicodae”, “Phylogenomic analyses for Andropogoneae”, “Phylogenomic analyses for Chloridoideae”, “Phylogenomic analyses for Boutelouodinae”, and “Phylogenomic analyses for Gouiniodinae and Eragrostideae”.Datasets for MAPS analyses are available in the folder of ‘MAPS’. Datasets for Supplementary Figure 32 are available in the folder of “Bamboo Genome Analyses”. Datasets for ASTRAL analyses of pruned subtrees for <i>Oryza</i> are available in the folder of “ASTRAL analyses of pruned subtrees for <i>Oryza</i>” (Supplementary Figure 43).In addition, the code of species used in our study can be found in the PDF file of “WGD”.