Motivation: Quality of gene expression analyses using de novo assembled transcripts in species that experienced recent polyploidization remains unexplored. Results: Differential gene expression (DGE) analyses using putative genes inferred by Trinity, Corset and Grouper performed slightly differently across five plant species that experienced various poly-ploidy histories. In species that lack recent polyploidy events that occurred in the past several millions of years, DGE analyses using de novo assembled transcriptomes identified 54–82% of the differen-tially expressed genes recovered by mapping reads to the reference genes. However, in species that experienced more recent polyploidy events, the percentage decreased to 21–65%. Gene co-expression network analyses using de novo assemblies vs. mapping to the reference genes recov-ered the same module that significantly correlated with treatment in one species that lacks recent polyploidization.

1.4_Trinity_assemblies.tarDe novo transcriptome assemblies from five species1.6_reference_base_coverage.tarThe sequencing depth files generated by Samtools. The files were used to calculate the total number of reference bases, the number and proportion of expressed reference bases2.2_2.3_getting_Corset_Grouper_cluster_information.tar.gzFiles used to generate Corset and Grouper clusters5_evaluate_dge.tar.gzfiles that used for evaluating the DGE analyses for wheat. RNA seq data were from Li et al. (2019)6_gene_coexpression_WGCNA.tar.gz3.2_evaluating_clustering.tarClusters and files used to evaluate quality of clustersReadme