Correcting for Differential Transcript Coverage Reveals a Strong Relationship between Alternative Splicing and Organism Complexity

Abstract

What at the genomic level underlies organism complexity? Although several genomic features have been associated with organism complexity, in the case of alternative splicing, which has long been proposed to explain the variation in complexity, no such link has been established. Here, we analyzed over 39 million expressed sequence tags available for 47 eukaryotic species with fully sequenced genomes to obtain a comparable index of alternative splicing estimates, which corrects for the distorting effect of a variable number of transcripts per species—an important obstacle for comparative studies of alternative splicing. We find that alternative splicing has steadily increased over the last 1,400 My of eukaryotic evolution and is strongly associated with organism complexity, assayed as the number of cell types. Importantly, this association is not explained as a by-product of covariance between alternative splicing with other variables previously linked to complexity including gene content, protein length, proteome disorder, and protein interactivity. In addition, we found no evidence to suggest that the relationship of alternative splicing to cell type number is explained by drift due to reduced Ne in more complex species. Taken together, our results firmly establish alternative splicing as a significant predictor of organism complexity and are, in principle, consistent with an important role of transcript diversification through alternative splicing as a means of determining a genome’s functional information capacity.

Alternative splicing and the evolution of phenotypic novelty

“…Here, we have summarized the evidence for a prominent role for alternative splicing in functional genomic evolution. Unlike gene number [61], alternative splicing is, at present, the foremost genomic predictor of increases in developmental complexity (using the number of cell types as proxy) [62]. It remains an open question as to what extent the association of alternative splicing and the number of distinct cell types is functional, or potentially a byproduct of the fact that more complex organisms have lower effective population sizes and so are subject more strongly to genetic drift.…”

“…[61,62]), alternative splicing-as a mechanism allowing transcript diversification in the absence of increases in gene number-is a prime candidate to explain the G-value paradox [37,38,40,63]. Comparative studies have reported marked differences in the prevalence of alternative splicing across eukaryotic lineages as well as a significant correlation between alternative splicing and the number of cell types per species [39,61,62,64]. These results are in principle consistent with an adaptive role of alternative splicing in determining a genome's functional information capacity and facilitating transcript diversification in species with greater numbers of cell types.…”

“…Although compendia of effective population size data have developed substantially [93,94], there is still minimal overlap with the set of species for which comparative alternative splicing levels have been estimated. Taking adult body weight [95], average age at sexual maturity [96] and generation time [97] as proxies of effective population size [89] as well as 'effective information' (a value derived from principles of information theory as 'the minimal amount of genomic information needed to construct an organism') [98], the correlation of alternative splicing and cell-type number remains significant [62] (table 1 and electronic supplementary material, table S1). …”

The number of cell types, information content, and the evolution of complex multicellularity

“…The number of different cell types characterizing an organism has been used to measure organismic complexity because it quantifies the extent to which cellular structure is differentiated into phenotypically different entities (e.g., [1][2][3][4][5]), because this approach is indifferent to whether an organism is a fungus, plant, or animal, and because it is insensitive to most methods of categorizing grade or clade levels of organization. It can even be used to quantify the complexity of unicellular organisms because the vast majority of species with this body plan achieve different cell functionalities and morphologies at different stages in their life cycles (e.g., resting cysts versus actively motile cells).…”

Similar ratios of introns to intergenic sequence across animal genomes

“…These data from O. bimaculoides suggested that overall patterns in splicing do not display a reliable connection to organismic complexity when complexity is generalized across animal groups. However, without proper measurements of cell types from the octopus, it cannot be assumed that the number of cell types resembles the value for the fruit fly, which was implicit in other studies given that all protostomes were effectively represented by insects (Chen et al 2014). Thus, it could be the case that the octopus, with a large genome, has a large number of cell types and many genes are spliced, all in agreement with the splicingcomplexity hypothesis.…”