Aberrant regulation of RNA splicing in sunflower hybrids may underlie intrinsic incompatibilities

Abstract

Alternative spicing is an integral part of gene expression in multicellular organisms that allows for diverse mRNA transcripts and proteins to be produced from a single gene. However, most existing analyses have focused on macro-evolution, with only limited research on splice site evolution over shorter term, micro-evolutionary time scales. Here we examine splicing evolution that has occurred during domestication and observe 45 novel splice forms with strongly transgressive isoform compositions, representing 0.24% of analyzed transcripts. We identify loci associated with variation in the levels of these splice forms, finding that many novel transcripts were regulated by multiple alleles with non-additive interactions. A subset of these interactions involved the expression of individual spliceosome components. These overdominant and epistatic interactions often resulted in alteration in the protein-coding regions of the transcripts, resulting in frameshifts and truncations. By associating the splice variation in these genes with size and growth rate measurements, we found that none of the individual splice variants affected these plant traits significantly, but the cumulative expression of all aberrant transcripts did show a significant reduction in growth rate associated with higher proportions of disrupted transcripts. This demonstrates the importance of co-evolution of the different spliceosomal components and their regulators and suggests that these genes may contribute to evolution of reproductive isolation as Bateson-Dobzhansky-Muller incompatibility loci. Author summaryIn multicellular organisms, it is common that segments of pre-mRNA molecules are physically removed, and the remaining segments are spliced back together. Through splicing alternative combinations of segments together, organisms produce various mRNA molecules, and thus multiple proteins, using the information encoded in a single gene. Here, we investigated the RNA of two sunflower genotypes, one wild and one domesticated, as well as the hybrid offspring resulting from a cross between the two genotypes. We found certain mRNA molecules that were spliced exclusively in the hybrids and were absent in the examined parental lines. These unique hybrid mRNAs were predicted to be consequential for the hybrids health, and thus represented a malfunction in the mechanisms that regulate splicing. These results improve our understanding of the genetic regulation of alternative splicing and how alternative splice forms evolve. Our findings may lead to further inquiries about how aberrant splicing promotes the formation of new species in nature.