Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs

Abstract

Background: Alternative splicing is an important mechanism for generating functional and evolutionary diversity of proteins in eukaryotes. Here, we studied the frequency and functionality of recently gained, rodent-specific alternative exons.

Results: We projected the data about alternative splicing of mouse genes to the rat, human, and dog genomes, and identified exons conserved in the rat genome, but missing in more distant genomes. We estimated the frequency of rodent-specific exons while controlling for possible residual conservation of spurious exons. The frequency of rodent-specific exons is higher among predominantly skipped exons and exons disrupting the reading frame. Separation of all genes by the rate of sequence evolution and by gene families has demonstrated that rodent-specific cassette exons are more frequent in rapidly evolving genes and in rodent-specific paralogs.

Conclusion: Thus we demonstrated that recently gained exons tend to occur in fast-evolving genes, and their inclusion rate tends to be lower than that of older exons. This agrees with the theory that gain of alternative exons is one of the major mechanisms of gene evolution.

Figure 1

Conservation of mouse frame-preserving (left) and frame-disrupting (right) cassette exons with different inclusion level in human, dog and rat genomes for different groups of genes: (A, B, C) rapidly, moderately, and slowly evolving genes, respectively. Top plots: blue diamonds, red squares and green triangles – the fraction of mouse cassette exons conserved in the human, dog and rat genomes, respectively. Crescent pie charts below: the segment sizes are proportional to the number of exons conserved in the human, dog and rat genomes (grey), exons conserved in the rat genome and in the human or dog genome but not both (blue and red, respectively), exons conserved only in the rat genome (dark green for estimated functional conservation, brown for residual conservation, see the text for details), mouse-specific exons (green).