Data from: Transcriptome analysis indicates considerable divergence in alternative splicing between duplicated genes in Arabidopsis thaliana

Using RNA-seq we investigated the degree to which alternative splicing patterns are conserved between duplicated genes in Arabidopsis thaliana. Our results revealed that 30% of AS events in alpha whole genome duplicates, and 33% of AS events in tandem duplicates, are qualitatively conserved within leaf tissue. Loss of ancestral splice forms, as well as asymmetric gain of new splice forms, may account for this divergence.

Conserved events had different frequencies, as only 31% of shared AS events in alpha whole genome duplicates and 41% of shared AS events in tandem duplicates had similar frequencies in both paralogs, indicating considerable quantitative divergence. Analysis of published RNA-seq data from nonsense mediated decay (NMD) mutants indicated that 85% of alpha whole genome duplicates and 89% of tandem duplicates have diverged in their AS-induced NMD.

Our results indicate that alternative splicing shows a high degree of divergence between paralogs such that qualitatively conserved alternative splicing events tend to have quantitative divergence. Divergence in AS patterns between duplicates may be a mechanism of regulating expression level divergence.

Usage notes

Repo for Tack et al. 2014 Genetics Data and scripts from "Transcriptome Analysis Indicates Considerable Divergence in Alternative Splicing Between Duplicated Genes in Arabidopsis thaliana" Github_Dryad_repo.zip