Different levels of alternative splicing among eukaryotes

Abstract

Alternative splicing increases transcriptome and proteome diversification. Previous analyses aiming at comparing the rate of alternative splicing between different organisms provided contradicting results. These contradicting results were attributed to the fact that both analyses were dependent on the expressed sequence tag (EST) coverage, which varies greatly between the tested organisms. In this study we compare the level of alternative splicing among eight different organisms. By employing an EST independent approach we reveal that the percentage of genes and exons undergoing alternative splicing is higher in vertebrates compared with invertebrates. We also find that alternative exons of the skipping type are flanked by longer introns compared to constitutive ones, whereas alternative 5' and 3' splice sites events are generally not. In addition, although the regulation of alternative splicing and sizes of introns and exons have changed during metazoan evolution, intron retention remained the rarest type of alternative splicing, whereas exon skipping is more prevalent and exhibits a slight increase, from invertebrates to vertebrates. The difference in the level of alternative splicing suggests that alternative splicing may contribute greatly to the mammal higher level of phenotypic complexity, and that accumulation of introns confers an evolutionary advantage as it allows increasing the number of alternative splicing forms.

Figure 1

EST-dependent analysis of the levels of alternatively spliced genes and exons among eukaryotes. Percentage of alternatively spliced exons (A) and genes (B) among eight different organisms. The percentages were calculated based on the analysis of UniGene clusters using all reliable data available.

Figure 2

Minimization of the dependence on EST coverage by randomizations. Percentage of alternatively spliced exons (A) and genes (B) among eight different organisms. Percentages were calculated based on the analysis of UniGene clusters, after removing mRNA data. Ten ESTs were randomly selected and this analysis repeated 100 times for each cluster.

Figure 3

Use of homologous clusters and MGC ESTs. Percentage of alternatively spliced exons (A) and genes (B) among eight different organisms. Percentages were calculated based on the analysis of UniGene clusters, using only ESTs derived from the MGC project. The analysis was performed on homologous human/mouse clusters, where both contained at least 10 ESTs, and 10 ESTs were repeatedly randomly selected.

Figure 4

Relative prevalence of the different types of alternatively spliced exons in different species. The relative prevalence of the four types of alternatively spliced exons (exon skipping, alternative 3′ss, alternative 5′ss and intron retention) are shown for the different organisms.