Alternative splicing and the evolution of phenotypic novelty

Abstract

One contribution of 17 to a theme issue 'Evo-devo in the genomics era, and the origins of morphological diversity'. Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative splicing to developmental programmes. The role of alternative splicing as a source of transcript diversification has previously been compared to that of gene duplication, with the relationship between the two extensively explored. Alternative splicing is reduced following gene duplication with the retention of duplicate copies higher for genes which were alternatively spliced prior to duplication. Furthermore, and unlike the case for overall gene number, the proportion of alternatively spliced genes has also increased in line with the evolutionary diversification of cell types, suggesting alternative splicing may contribute to the complexity of developmental programmes. Together these observations suggest a prominent role for alternative splicing as a source of functional innovation. However, it is unknown whether the proliferation of alternative splicing events indeed reflects a functional expansion of the transcriptome or instead results from weaker selection acting on larger species, which tend to have a higher number of cell types and lower population sizes.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.

Modulation of Yorkie activity by alternative splicing is required for developmental stability

“…Alternative splicing of pre-messenger RNAs is recognized as a major source of transcriptomic and proteomic diversity 31,32 . Its extent correlates with organism complexity 33 and several examples illustrate that alternative splicing is a source of phenotypic novelty during evolution 34 . Here we provide an experimental evidence that alternative splicing also participates in the process of canalization, which reflects the resistance of a phenotype to genetic and/or environmental perturbations 35 .…”

Novel alternative splicing variants of <i>ACOX1</i> and their differential expression patterns in goats

“…As a major mechanism for the expansion of transcriptome and proteome diversity (Bush et al, 2017), AS is a principal contributor to the evolution of phenotypic complexity in mammals. This type of evolution was also demonstrated for the ACOX1 gene, a rate-limiting and relatively conserved enzyme in the peroxisomal fatty β-oxidation pathway.…”

Perspectives on the history of evo-devo and the contemporary research landscape in the genomics era

“…The issue begins with articles about various aspects of genomics, with Holland et al [26] discussing gene duplication and Urrutia and co-workers [51] alternative splicing and their contributions to phenotypic innovation while Orlando and co-workers [47] outline the latest methodologies that allow analysis of fossil genomes. Tschopp & Tabin [25] consider the impact of genomics on the concept of deep homology.…”

“…Recent comparative studies of transcriptome profiles identifying alternative splicing events suggest a potentially important role for this process in the evolution of phenotypic plasticity and phenotypic innovation, as reviewed by Bush et al [51]. However, the adaptive relevance of transcript diversification mediated by alternative splicing remains unclear [60,61].…”