Transcriptome Analysis Indicates Considerable Divergence in Alternative Splicing Between Duplicated Genes inArabidopsis thaliana

Abstract

Gene and genome duplication events have created a large number of new genes in plants that can diverge by evolving new expression profiles and functions (neofunctionalization) or dividing extant ones (subfunctionalization). Alternative splicing (AS) generates multiple types of mRNA from a single type of pre-mRNA by differential intron splicing. It can result in new protein isoforms or downregulation of gene expression by transcript decay. 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 a-wholegenome 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 a-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 nonsensemediated decay (NMD) mutants indicated that 85% of a-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.

Alternative splicing enhances transcriptome complexity in desiccating seeds

“…Prediction of AS on proteasome complexity AS has the potential to rapidly expand proteasome complexity and had a crucial role during plant evolution (Tack et al 2014;Vitulo et al 2014;Xu et al 2014;Li et al 2015;Xiao et al 2015). To gain information about the possible effects of AS during seed desiccation, we predicted the sequences of the protein isoforms resulting from the IR AS transcripts.…”

Evolution of Gene Duplication in Plants

“…For example, in hexaploid bread wheat, 42% and 61% of alternative splicing events differ between homologous gene pairs in chromosome 3A-3B and 3A-3D comparisons, respectively (Akhunov et al, 2013). In Arabidopsis, 85% of a WGD and 89% of tandem duplicates have divergent alternatively spliced forms (Tack et al, 2014).…”

The Evolutionary Relationship between Alternative Splicing and Gene Duplication

“…Such mutations could be a replacement of AS events and therefore AS events are lost quickly. Tack et al (2014) studied different WGD and tandem duplications in A. thaliana looking for the qualitative and quantitative conservation of AS events in paralogs. Such conservation was higher in paralogous genes resulting from tandem duplications than from WGD-resulting paralogs.…”