The organization and evolution of the dipteran and hymenopteran Down syndrome cell adhesion molecule (Dscam) genes

Abstract

The Drosophila melanogaster Down syndrome cell adhesion molecule (Dscam) gene encodes an axon guidance receptor and can generate 38,016 different isoforms via the alternative splicing of 95 variable exons. Dscam contains 10 immunoglobulin (Ig), six Fibronectin type III, a transmembrane (TM), and cytoplasmic domains. The different Dscam isoforms vary in the amino acid sequence of three of the Ig domains and the TM domain. Here, we have compared the organization of the Dscam gene from three members of the Drosophila subgenus (D. melanogaster, D. pseudoobscura, and D. virilis), the mosquito Anopheles gambiae, and the honeybee Apis mellifera. Each of these organisms contains numerous alternative exons and can potentially synthesize tens of thousands of isoforms. Interestingly, most of the alternative exons in one species are more similar to one another than to the corresponding alternative exons in the other species. These observations provide strong evidence that many of the alternative exons have arisen by reiterative exon duplication and deletion events. In addition, these findings suggest that the expression of a large Dscam repertoire is more important for the development and function of the insect nervous system than the actual sequence of each isoform.

FIGURE 1.

Overview of Dscam genes from D. melanogaster, D. pseudoobscura, D. virilis, A. gambiae, and A. mellifera. The exon–intron organization of the Dscam gene from each organism is shown. The black exons are constitutively spliced. The alternative exons in the exon 4, 6, 9, and 17 clusters are shaded in red, purple, green, and blue, respectively. The number of variable exons within each cluster in each organism is indicated below each cluster. The exon 10 clusters in A. gambiae and A. mellifera correspond to the exon 9 cluster in the Drosophila species. The exon 14 and 22 clusters in A. gambiae and A. mellifera, respectively, correspond to the exon 17 clusters in the Drosophila species.

FIGURE 2.

Percent identity plot of the nucleotide sequence of the insect Dscam genes. The nucleotide sequences of the Dscam genes from D. melanogaster, D. pseudoobscura, D. virilis, A. gambiae, and A. mellifera were aligned using MultiPipmaker (Schwartz et al. 2000; http://bio.cse.psu.edu/pipmaker/). The locations of the exons in the D. melanogaster Dscam gene are shown on the top of the alignment. Each box depicts regions in the Dscam gene of the indicated organism that are 50%–100% identical to the D. melanogaster gene. The exon 4, 6, 9, and 17 clusters are colored in red, blue, green, and orange, respectively.

FIGURE 3.

Evolutionary relationships of the variable exons between D. melanogaster, D. pseudoobscura, and D. virilis. Each variable exon was conceptually translated. For each cluster, the amino acid sequences of each variable exon from each species were aligned using ClustalW and phylogenetic trees generated using MacVector with the UPGMA method. Branches containing D. melanogaster, D. pseudoobscura, and D. virilis sequences are colored in blue, red, and green, respectively. The branches are colored until two different species intersect. Separate trees were generated for the exon 4 cluster (A), the exon 6 cluster (B), and the exon 9 cluster (C).

FIGURE 4.

Evolutionary relationships of the variable exons between D. melanogaster, A. gambiae, and A. mellifera. Phylogenetic trees were generated as described in Figure 3 ▶ and Materials and Methods. Branches containing D. melanogaster, A. gambiae, and A. mellifera sequences are colored in blue, green, and red, respectively. The branches are colored until two different species intersect. Separate trees were generated for the exon 4 cluster (A), the exon 6 cluster (B), the exon 9 cluster (C), and the exon 17 cluster (D).