Evolution of alternative splicing in newly evolved genes of Drosophila

Abstract

New gene origination is a fundamental process underlying evolution of biological diversity. Although new genes usually evolve rapidly in sequences, structure and expression, the evolutionary pattern of alternative splicing (AS) in new genes and the molecular mechanisms involved in this alternation remain to be explored. Here, we used the new genes identified in the Drosophila melanogaster lineage to study alternation of AS and the possible functional consequences of these genes. We found that new genes tended to exhibit low degree of AS, though a few new genes were alternatively spliced. Interestingly loss of introns in retroposed new genes can only account for one third of the low-level AS in new genes, while partial gene duplication without AS exons and mutations in the duplicated AS exons/introns together have resulted in two-third AS losses in new genes, indicating that reducing the degree of AS is a general trend in all categories of new genes. Further investigations on tissue expression patterns of these new genes showed that those with AS alternation had a relatively lower expression level, were expressed in fewer tissues and tended to be more likely expressed in testis than their parental genes. All these observations imply that these new genes may have gained diverged structures and expression patterns from their parental genes after AS alternation.

Introduction

Origin of new genes with novel functions is a fundamental process underlying evolution of organisms. The molecular mechanisms involved in the generation of new genes include gene duplication, retroposition, exon shuffling, lateral gene transfer, gene fusion/fission and de novo origination (Long et al., 2003, Zhou & Wang, 2008), among which gene duplication was considered to provide the major source for genetic novelties (Ohno, 1970, Gu et al., 2002, Katju & Lynch, 2006, Zhou et al., 2008). Formation of chimeric gene structures and expression differentiation in different tissues have been proposed to account for the functional divergence between parental and young duplicates (Gu et al., 2002, Wang et al., 2006, Zhou et al., 2008).

Another fundamental process underlying transcriptome and proteome diversity is alternative splicing at transcriptional level (Ast, 2004, Xing & Lee, 2006, Keren et al., 2010), while gene duplication contributes to such diversity at DNA level. How gene duplication and alternative splicing interact during the course of evolution is an interesting question. Previous studies on AS evolution in duplicated genes, which were mainly based on old duplicates, have observed that there is a negative correlation between the mean number of AS isoforms and gene family size (Kopelman et al., 2005, Su et al., 2006, Jin et al., 2008). Three alternative explanations accounting for this negative correlation between number of AS isoforms and the gene family size, (1) genes with few splice variants preferentially tend to duplicate, (2) the process of gene duplication causes AS to be lost, (3) after gene duplication, subsequent evolution preferentially favors AS loss. However, if the duplication event occurred a long time ago, it would be hard to distinguish which of these three hypotheses had attributed to the negative correlation.

Beyond this simple observation, another relevant and more important question is whether new genes tend to evolve new AS forms or lose AS forms after origination compared to the parental genes. Some well studied new genes showed alternation of AS. A typical example is sphinx, which originated as a retroposed sequence of the ATP synthase chain F gene and recruited a nearby exon and intron, thereby evolving a chimeric gene structure and sex- and development-specific alternative splicing (Wang et al., 2002). Another example is Sdic, which is also a chimeric gene derived from a duplication and fusion of the gene AnnX and Cdic (Nurminsky et al., 1998a, Nurminsky et al., 1998b, Ranz et al., 2003, Ponce & Hartl, 2006). The parental gene, Cdic, is alternatively spliced, while Sdic has only one splicing forms (Nurminsky et al., 1998a). In spite of these, little is known about the evolutionary patterns of alternative splicing (AS) changes in newly evolved young genes. In this study, young genes will not only allow us to discover the general evolutionary pattern of AS but also address the molecular mechanisms of AS alternation in newly duplicated genes. Finally, it is also of interest to understand the consequences of AS alternation in new genes. Intuitively AS alternation could lead to change of gene structures. In this study we examined the impacts of AS changes on protein domains, regulatory elements and expression patterns in AS altered new genes comparing to their parental genes.