The evolution of Dscam genes across the arthropods

<p>Abstract</p> <p>Background</p> <p>One way of creating phenotypic diversity is through alternative splicing of precursor mRNAs. A gene that has evolved a hypervariable form is <it>Down syndrome cell adhesion molecule </it>(<it>Dscam-hv</it>), which in <it>Drosophila melanogaster </it>can produce thousands of isoforms via mutually exclusive alternative splicing. The extracellular region of this protein is encoded by three variable exon clusters, each containing multiple exon variants. The protein is vital for neuronal wiring where the extreme variability at the somatic level is required for axonal guidance, and it plays a role in immunity where the variability has been hypothesised to relate to recognition of different antigens. <it>Dscam-hv </it>has been found across the Pancrustacea. Additionally, three paralogous non-hypervariable <it>Dscam-like </it>genes have also been described for <it>D. melanogaster</it>. Here we took a bioinformatics approach, building profile Hidden Markov Models to search across species for putative orthologs to the <it>Dscam </it>genes and for hypervariable alternatively spliced exons, and inferring the phylogenetic relationships among them. Our aims were to examine whether <it>Dscam </it>orthologs exist outside the Bilateria, whether the origin of <it>Dscam-hv </it>could lie outside the Pancrustacea, when the <it>Dscam-like </it>orthologs arose, how many alternatively spliced exons of each exon cluster were present in the most common recent ancestor, and how these clusters evolved.</p> <p>Results</p> <p>Our results suggest that the origin of <it>Dscam </it>genes may lie after the split between the Cnidaria and the Bilateria and supports the hypothesis that <it>Dscam-hv </it>originated in the common ancestor of the Pancrustacea. Our phylogeny of <it>Dscam </it>gene family members shows six well-supported clades: five containing <it>Dscam-like </it>genes and one containing all the <it>Dscam-hv </it>genes, a seventh clade contains arachnid putative <it>Dscam </it>genes. Furthermore, the exon clusters appear to have experienced different evolutionary histories.</p> <p>Conclusions</p> <p><it>Dscam </it>genes have undergone independent duplication events in the insects and in an arachnid genome, which adds to the more well-known tandem duplications that have taken place within <it>Dscam-hv </it>genes. Therefore, two forms of gene expansion seem to be active within this gene family. The evolutionary history of this dynamic gene family will be further unfolded as genomes of species from more disparate groups become available.</p

Quantitative Profiling of Drosophila melanogaster Dscam1 Isoforms Reveals No Changes in Splicing after Bacterial Exposure

The hypervariable Dscam1 (Down syndrome cell adhesion molecule 1) gene can produce thousands of different ectodomain isoforms via mutually exclusive alternative splicing. Dscam1 appears to be involved in the immune response of some insects and crustaceans. It has been proposed that the diverse isoforms may be involved in the recognition of, or the defence against, diverse parasite epitopes, although evidence to support this is sparse. A prediction that can be generated from this hypothesis is that the gene expression of specific exons and/or isoforms is influenced by exposure to an immune elicitor. To test this hypothesis, we for the first time, use a long read RNA sequencing method to directly investigate the Dscam1 splicing pattern after exposing adult Drosophila melanogaster and a S2 cell line to live Escherichia coli. After bacterial exposure both models showed increased expression of immune-related genes, indicating that the immune system had been activated. However there were no changes in total Dscam1 mRNA expression. RNA sequencing further showed that there were no significant changes in individual exon expression and no changes in isoform splicing patterns in response to bacterial exposure. Therefore our studies do not support a change of D. melanogaster Dscam1 isoform diversity in response to live E. coli. Nevertheless, in future this approach could be used to identify potentially immune-related Dscam1 splicing regulation in other host species or in response to other pathogens.status: publishe