Gene duplication, tissue-specific gene expression and sexual conflict in stalk-eyed flies (Diopsidae)

Abstract

Gene duplication provides an essential source of novel genetic material to facilitate rapid morphological evolution. Traits involved in reproduction and sexual dimorphism represent some of the fastest evolving traits in nature, and gene duplication is intricately involved in the origin and evolution of these traits. Here, we review genomic research on stalk-eyed flies (Diopsidae) that has been used to examine the extent of gene duplication and its role in the genetic architecture of sexual dimorphism. Stalk-eyed flies are remarkable because of the elongation of the head into long stalks, with the eyes and antenna laterally displaced at the ends of these stalks. Many species are strongly sexually dimorphic for eyespan, and these flies have become a model system for studying sexual selection. Using both expressed sequence tag and next-generation sequencing, we have established an extensive database of gene expression in the developing eye-antennal imaginal disc, the adult head and testes. Duplicated genes exhibit narrower expression patterns than non-duplicated genes, and the testes, in particular, provide an abundant source of gene duplication. Within somatic tissue, duplicated genes are more likely to be differentially expressed between the sexes, suggesting gene duplication may provide a mechanism for resolving sexual conflict.

Figure 1.

Identifying sex-linkage in T. dalmanni. (a) Distribution of T. dalmanni CGH log₂ ratio values. Male and female genomic DNA was hybridized to microarray slides containing probes designed from EST sequence data. A total of 3444 genes are represented. The large peak indicates autosomal genes while the smaller peak are genes on the X chromosome. (b) T. dalmanni chromosomal synteny with D. melanogaster indicates the diopsid X chromosome is homologous to chromosome 2L in Drosophila. The autosomal category includes 2891 T. dalmanni genes and the X chromosome comprises 533 T. dalmanni genes.

Figure 2.

The relationship between gene duplication and tissue specificity of gene expression in T. dalmanni. Columns indicate the percentage of genes for a given tissue expression pattern that are composed of genes that have undergone a gene duplication. The numbers within the columns provide the total number of duplicate paralogues that fall within that expression category. Tissue-‘enriched’ genes are defined as genes that are expressed five times more than in the other tissue and tissue-‘specific’ genes are expressed 500 times more than in the other tissue.

Figure 3.

Association between chromosomal location and tissue specificity of gene expression. ‘2L’ genes in T. dalmanni have homologues on chromosome 2L in D. melanogaster, which is the source of the neo-X chromosome in T. dalmanni. ‘Non-2L’ genes in T. dalmanni have homologues on other chromosomes in D. melanogaster. Tissue-‘enriched’ genes are defined as genes that are expressed five times more than in the other tissue. A gene was scored as tissue-enriched if any of the paralogues associated with that gene was expressed five times more in one of the tissues, whereas ‘ubiquitous’ genes included only genes for which no paralogues were tissue-enriched. Dark grey bars, 2L; light grey bars, non-2L. p < 0.0001.

Figure 4.

Phylogenetic analysis of α-tubulin genes in Diptera. Bootstrap values are provided for nodes defining and joining stalk-eyed fly paralogues. Dm, D. melanogaster, Dp, D. pseudoobscura, Sb, S. beccarri, Td (Cam), T. dalmanni (Cameron population), Td (Gom), T. dalmanni (Gombak population), Td (Lang), T. dalmanni (Langat population), Tq, T. quinqueguttata, Tt, T. thaii, Tw, T. whitei. Measurements of gene expression values (RPKM) are presented for each T. dalmanni (Gom) paralogue.

Figure 5.

Phylogenetic analysis of β-tubulin genes in Diptera. Bootstrap values are provided for nodes defining and joining stalk-eyed fly paralogues. Dm, D. melanogaster; Dp, D. pseudoobscura; Sb, S. beccarri; Td (Cam), T. dalmanni (Cameron population); Td (Gom), T. dalmanni (Gombak population); Td (Lang), T. dalmanni (Langat population); Tq, T. quinqueguttata; Tt, T. thaii; Tw, T. whitei. Measurements of gene expression values (RPKM) are presented for each T. dalmanni (Gom) paralogue, along with the sequence data for two important functional domains (see text for details). The axoneme motif in the C-terminal tail is underlined.

Figure 6.

Association between sex-biased gene expression and gene duplication. Black bars, duplicates; grey bars, non-duplicates. ‘Duplicates’ include all paralogues for any gene that has duplicated in T. dalmanni; ‘non-duplicates’ have not been involved in a gene duplication event. Bars indicate the percentage of genes in each category that exhibit twofold or fourfold expression differences between males and females in the adult head. Black bars, duplicates; grey bars, non-duplicates. ***p < 0.0001.

Figure 7.

Phylogenetic analysis and gene expression values for two genes—Fer1HCH (a) and Ance-4 (b)—that have duplicated and exhibit sex-biased gene expression in the adult head of T. dalmanni. In the gene expression boxes, M, male head; F, female head; T, testes. Dm, D. melanogaster; Dp, D. pseudoobscura; Sb, S. beccarri; Tq, T. quinqueguttata.

Figure 8.

Rate of protein evolution for sex-biased and duplicated genes in the adult head. All genes that are expressed five times more in the testes were excluded from the analysis. ‘Sex-biased’ indicates genes with twofold expression differences between the sexes. Dark grey bars, unbiased; light grey bars, sex-biased. Dm, D. melanogaster.