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Data from: Performance of gene expression analyses using de novo assembled transcripts in polyploid species

Cite this dataset

Chen, Lingyun; Morales-Briones, Diego F.; Passow, Courtney N.; Yang, Ya (2019). Data from: Performance of gene expression analyses using de novo assembled transcripts in polyploid species [Dataset]. Dryad. https://doi.org/10.5061/dryad.4p6n481

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.

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