Data from: Performance of gene expression analyses using de novo assembled transcripts in polyploid species
Data files
Sep 11, 2019 version files 3.06 GB
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1.4_Trinity_assemblies.tar.gz
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1.6_reference_base_coverage.tar.gz
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2.2_2.3_getting_Corset_Grouper_cluster_information.tar.gz
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3.2_evaluating_clustering.tar.gz
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5_evaluate_dge.tar.gz
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6_gene_coexpression_WGCNA.tar.gz
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README.txt
Abstract
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.